PromoterCAD: Data Driven Design of Plant Regulatory DNA｜Mash up the Linked Open Data

about this App

PromoterCAD: Data Driven Design of Plant Regulatory DNA

if (typeof Application == "undefined" || !Application) {
	var Application = {};
}

Application.genocon = function() {
	this._init.apply(this, arguments);
};

Application.genocon.prototype = {
	
	CHAR_SEQ_EMPTY : "-",
	
	_baseSequence : null,
	_tooltip : null,
	_methodList : null,
	_appBaseLineSequence : null,
	_appMenuHandler : null,
	_validCharcters : ['A','T','C','G','-'],
	
	_default : {
		baseSequenceContainerId : "baseSequenceContainer",
		fixedSequenceClass : "fixedSequence",
		finishSequence : "finishSequence",
		finishSequenceContainer : "finishSequenceContainer",
		baseErrorMessageClass : "baseErrorMessage",
		errorMessageEnterSequence : "Please enter a sequence of minimum length {0}",
		errorMessageMaximumSequence : "Please enter a sequence of maximum length {0}",
		useButtonClass : "useButton",
		nextButtonClass : "nextButton",
		finishNowButtonClass : "finishNow",
		nextButtonContainerClass : "nextButtonContainer",
		collapseButton : "collapseButton",
		expandButton : "expandButton",
		removeButton : "removeButton",
		appContainerClass : "applicationContainer",
		appDataContainerClass : "applicationDataContainer",
		actionButtonContainer : "actionButtonContainer",
		actionResultContainer : "actionResultContainer",
		baseSequenceBoxClass : "baseSequenceBox",
		baseSequenceClass : "baseSequence",
		selectDataBaseList : "databaseList",
		selectMethodList : "optionList",
		databaseFilteringProperty : "#motif%20sequence",
		methodUrlProperty : "#application%20URL",
		baseSequenceMinLength : 50,
		baseSequenceMaxLength : 500,
		//applicationOptionClass : "applicationOptionRadio",
		analysisMethodComboClass : "analysisMethod",
		expressionDbComboClass : "expressionDb",
		dataColomboClass : "dataCol",
		analysisMethodContainer : "analysisMethodContainer",
		expressionDbContainer : "expressionDbContainer",
		dataColContainer : "dataColContainer",
		chkEmptySequenceId : "chkEmptySequnce",
		analysisMethodComboEmptyOptionText : "-- Select Analysis Method --",
		expressionDbComboEmptyOptionText : "-- Select Expression Database --",
		dataColColomboEmptyOptionText : "-- Select Data Collection --",
		manualMotifEntryToolName : "InputMotif",
		itemLabelPostfix : "Label",
		finishSequenceFixedClass : "finishSequenceFixed",
		repeatButtonClass : "repeatAgain",
		baseSequenceErrDivClass : "baseSequenceError"
	},
	
	_tag : {
		databaseTag : "database",
		methodTag : "method"
	},
	
	_tooltipName : {
		atGeneExpress : "atgenexpress",
		diurnal : "diurnal",
		selectDatabase : "selectdatabase",
		selectTool : "Select Tool",
		motifExpress : "motifexpress",
		motifCircatian : "motifcircadian",
		motifRank : "motifranking",
		motifQuery : "motifquery",
		inputMotif : "inputmotif",
		defaultSequence : "Base Sequence",
		fixedSequence : "gacccttcctctatataaggaagttcatttcatttggagaggacctcgac",
		finishNow : "Finish Now",
		next : "Next",
		expressionDb : "Expression Database",
		analysisMethod : "Analysis Method",
		dataCollection : "Data Collection",
		baseSequence : "Base Sequence",
		finishNow : "Finish Now",
		startButton : "Start"
	},
	
	_init : function() {
		this._methodList = [];
		this._initToolTip();
		this._initDefaultSequence();
		this._initAppBaseLineSequence();
		this._initLoadScript();
		this._initUseButtonListener();
		this._initAppMenuHanndler();
		this._initAnalysisMethodListener();
		this._initExpressionDbListener();
		this._initDataCollectionListener();
		this._initEmptySequenceCheckBox();
	},
	
	_initToolTip : function() {
		this._tooltip = new Application.tooltip();
	},
	
	_initEmptySequenceCheckBox : function() {
		var self = this;
		$("#" + this._default.chkEmptySequenceId).click(function() {
			if ($(this).is(":checked")) {
				var textArea = $("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass)
				$(textArea).attr("value","");
				self._fillEmptyBaseSequence();
				$(textArea).attr("disabled",true);
				$("div." + self._default.baseSequenceErrDivClass).hide();
			} else {
				$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass).attr("disabled",false);
			}
		});
		/* following two lines were added to correct the behaviour, if user just pressed F5 button to 
           refresh the browser. in that case if previously checkbox is unnchecked, even after pressing
           F5, it remains unchecked in the new window
        */
		$("#" + this._default.chkEmptySequenceId).attr("checked","checked");
		$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass).attr("disabled",true);
	},
	
	_initDefaultSequence : function() {
		var self = this;
		this._fillEmptyBaseSequence();
		$baseInput = $("#" + this._default.baseSequenceContainerId + " ." + this._default.baseSequenceClass);
		$baseInput.attr("value",$baseInput.val());
		$baseInput.keyup(function() {
			$baseInput.attr("value", $baseInput.val());
		});
		$("#" + this._default.baseSequenceContainerId + " ." + this._default.baseSequenceBoxClass).scrollLeft(10000);
		var timer = new Application.timer();
		var applyToolTip = function() {
			var dToolTip = self._getToolTip(self._tooltipName.defaultSequence);
			var fToolTip = self._getToolTip(self._tooltipName.fixedSequence);
			var toolToolTip = self._getToolTip(self._tooltipName.selectTool);
			var analysisCmbToolTip = self._getToolTip(self._tooltipName.analysisMethod);
			var expDbToolTip = self._getToolTip(self._tooltipName.expressionDb);
			var dataCollToolTip = self._getToolTip(self._tooltipName.dataCollection);
			var startButToolTip = self._getToolTip(self._tooltipName.startButton);
			if (dToolTip && fToolTip) {
				var labelPostfix = self._default.itemLabelPostfix;
				//$("#tests").html(dataCollToolTip);
				//$("#tests").attr("title",$("#tests").html());
				$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass).attr("title", dToolTip);
				$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass + labelPostfix).attr("title", dToolTip);
				$("#" + self._default.baseSequenceContainerId + " ." + self._default.fixedSequenceClass).attr("title", fToolTip);
				
				$("." + self._default.appContainerClass + " ." + self._default.analysisMethodComboClass).attr("title", analysisCmbToolTip);
				$("." + self._default.appContainerClass + " ." + self._default.analysisMethodComboClass + labelPostfix).attr("title", analysisCmbToolTip);
				
				$("." + self._default.appContainerClass + " ." + self._default.expressionDbComboClass).attr("title", expDbToolTip);
				$("." + self._default.appContainerClass + " ." + self._default.expressionDbComboClass + labelPostfix).attr("title", expDbToolTip);
				
				$("." + self._default.appContainerClass + " ." + self._default.dataColomboClass).attr("title", dataCollToolTip);
				$("." + self._default.appContainerClass + " ." + self._default.dataColomboClass + labelPostfix).attr("title", dataCollToolTip);
				
				$("." + self._default.appContainerClass + " ." + self._default.selectMethodList).attr("title", toolToolTip);
				$("." + self._default.appContainerClass + " ." + self._default.selectMethodList + labelPostfix).attr("title", toolToolTip);
				
				$(" ." + self._default.useButtonClass).attr("title", startButToolTip);
			} else {
				timer.call(applyToolTip);
			}
		}
		applyToolTip();
	},
	
	_initAppBaseLineSequence : function() {
		this._appBaseLineSequence = new Application.baseLineSequence();
	},
	
	_initAppMenuHanndler : function() {
		this._appMenuHandler = new Application.MenuHandler()
	},
	
	_initLoadScript : function() {
		var self = this;
		var getFilesByTag = function(result) {
			$.each(result, function(workId, fileArray){
				$.each(fileArray, function(fileKey, fileName) {
					var getProperties = function(propertytList) {
						$.each(propertytList, function(propKey, propVal) {
							if (propVal.indexOf(self._default.methodUrlProperty) > -1) {
								self._loadPluginScriptList(workId, fileName, propVal);
								return false;
							}
						});
					}
					LinkData.getProperties(workId, fileName, getProperties);
					return false;
				});
			});
		}
		LinkData.getFilesByTag(null, self._tag.methodTag, getFilesByTag);
	},
	
	_initDefaultContainer : function() {
		this._initMethod();
		this._initActionButton();
		this._initMethodListener();
	},
	
	_initMethod : function() {
		var self = this;
		var $select = $("." + self._default.appContainerClass + " ." + self._default.selectMethodList);
		$("option", $select).remove();
		$select.append("<option value='-1' selected='selected'>-- Select Tool --</option>");
		$select.attr("title", self._getToolTip(self._tooltipName.selectTool));
		var getFilesByTag = function(result) {
			$.each(result, function(workId, fileArray){
				$.each(fileArray, function(fileKey, fileName) {
					var getSubjects = function(subjectList) {
						$.each(subjectList, function(subKey, subVal) {
							var label = self._getLabel(subVal);
							var tooltip = self._getToolTipByToolName(label);
							tooltip = (tooltip) ? tooltip : "";
							$select.append("<option value='" + label + "' title='" + tooltip + "'>" + label + "</option>");
							self._methodList.push(label);
						});
					}
					LinkData.getSubjects(workId, fileName, getSubjects);
				});
			});
		}
		LinkData.getFilesByTag(null, self._tag.methodTag, getFilesByTag);
	},
	
	_initActionButton : function() {
		var self = this;
		$("." + self._default.actionButtonContainer + " ." + self._default.collapseButton).click(function() {
			var parent = $(this).closest("." + self._default.appContainerClass);
			$(parent).find("." + self._default.appDataContainerClass).hide();
		});
		$("." + self._default.actionButtonContainer + " ." + self._default.expandButton).click(function() {
			var parent = $(this).closest("." + self._default.appContainerClass);
			$(parent).find("." + self._default.appDataContainerClass).show();
		});
		$("." + self._default.actionButtonContainer + " ." + self._default.removeButton).click(function() {
			if ($("." + self._default.appContainerClass).length == 1) {
				$("." + self._default.appContainerClass).hide();
				$("." + self._default.appContainerClass + " .actionResultContainer").html("");
				$("#" + self._default.baseSequenceContainerId + " ." + self._default.useButtonClass).show();
			} else {
				$(this).closest("." + self._default.appContainerClass).remove();
			}
		});
	},
	
	_scrollDown : function() {
		$("html, body").animate({ scrollTop: $(document).height() }, 1000);
	},
	
	// tool listner
	_initMethodListener : function() {
		var self = this;
		var $select = $("." + self._default.appContainerClass + " ." + self._default.selectMethodList);
		$select.change(function() {
			var selectedTool = $(this).val();
			if (selectedTool != "-1") {
				var parent = $(this).closest("." + self._default.appContainerClass);
				if (selectedTool == self._default.manualMotifEntryToolName) {
					//$(parent).find("." + self._default.applicationOptionClass).hide();
					self._showSelectedPlugin(null,$(this));
				} else {
					//self._clearWorkingArea(this);
					//self._initMotifExpressOptions(this);
					self._fillAnalysisMethodCombo(this);
					$(parent).find("." + self._default.analysisMethodContainer).show();
				}
				self._resetDataMiningCombos(this);
				self._scrollDown();
			}
		});
	},
	
	_makeTheDomChangeOfComboSelect : function(comboSelecter, value) {
		$(comboSelecter + " option").each(function(i){
        	var optionVal = $(this).val();
			if (optionVal == value) {
				$(this).attr("selected",true);
			}
    	});
	},
	
	_initAnalysisMethodListener : function() {
		var self = this;
		var selecter = "." + self._default.appContainerClass + " ." + self._default.analysisMethodComboClass;
		var $select = $(selecter);
		$select.change(function() {
			var selectedAnalysisMethod = $(this).val();
			if (selectedAnalysisMethod != "-1") {
				var parent = $(this).closest("." + self._default.appContainerClass);
				self._fillExpressionDBCombo(this);
				self._resetDataMiningCombos(this);
				$(parent).find("." + self._default.expressionDbContainer).show();
				self._scrollDown();
			}
		});
	},
	
	_initExpressionDbListener : function() {
		var self = this;
		var selector = "." + self._default.appContainerClass + " ." + self._default.expressionDbComboClass
		var $select = $(selector);
		$select.change(function() {
			var selectedExpressionDb = $(this).val();
			if (selectedExpressionDb != "-1") {
				var parent = $(this).closest("." + self._default.appContainerClass);
				self._fillDataCollectionCombo(this);
				self._resetDataMiningCombos(this);
				$(parent).find("." + self._default.dataColContainer).show();
				self._scrollDown();
			}
		});
	},
	
	_initDataCollectionListener : function() {
		var self = this;
		var selector = "." + self._default.appContainerClass + " ." + self._default.dataColomboClass;
		var $select = $(selector);
		$select.change(function() {
			var selectedDataCollection = $(this).val();
			if (selectedDataCollection != "-1") {
				self._showSelectedPlugin(selectedDataCollection,$(this));
				self._scrollDown();
			}
		});
	},
	
	_getSelectedTool : function(parentRef) {
		return $(parentRef).find("." + this._default.selectMethodList).val();
	},
	
	_getSelectedAnalysisMethod : function(parentRef) {
		var comboRef = $(parentRef).find("." + this._default.analysisMethodComboClass);
		if (comboRef.length > 0 && comboRef.is(":visible")) {
			return $(comboRef).val();
		} else {
			return "";
		}
	},
	/*
	_initMotifExpressOptions : function(context) {
		var self = this;
		var parent = $(context).closest("." + this._default.appContainerClass);
		//$(parent).find("." + self._default.applicationOptionClass).unbind('click');
		var selectedTool = $(context).val();
		if (selectedTool == "MotifExpress") {
			$(parent).find("." + self._default.applicationOptionClass).show();
			$(parent).find("." + self._default.applicationOptionClass).click(function() {
				var selectedDataCollection = $(parent).find("." + self._default.dataColomboClass);
				if ($(selectedDataCollection).is(":visible") && $(selectedDataCollection).val() != "-1") {
					self._showSelectedPlugin(selectedDataCollection.val(),$(this));
					//return;
				}	
			});
			// making motif max as the defaukt mthod
			$(parent).find("." + self._default.applicationOptionClass + " input[name=applicationOption]:checked")[0].checked=true;
		} else {
			$(parent).find("." + self._default.applicationOptionClass).hide();
		}
	},*/
	
	_resetDataMiningCombos : function(comboRef) {
		var parent = $(comboRef).closest("." + this._default.appContainerClass);
		var expressionDbContainer = $(parent).find("." + this._default.expressionDbContainer);
		var dataColContainer = $(parent).find(" ." + this._default.dataColContainer);
		var analysisMethodContainer = $(parent).find(" ." + this._default.analysisMethodContainer);
		var toolCombo = $(parent).find("." + this._default.selectMethodList);
		var comboClass = $(comboRef).attr("class");
		if (toolCombo.val() == this._default.manualMotifEntryToolName) {
			$(analysisMethodContainer).hide();
			$(expressionDbContainer).hide();
			$(dataColContainer).hide();
		} else {
			if (comboClass == this._default.selectMethodList) {
				$(analysisMethodContainer).show();
				$(expressionDbContainer).hide();
				$(dataColContainer).hide();
			} else if (comboClass == this._default.analysisMethodComboClass) {
				$(expressionDbContainer).hide();
				$(dataColContainer).hide();
			}
			$container = $(parent).find("." + this._default.actionResultContainer);
			$container.html("");
		}
		$(parent).find("." + this._default.finishSequenceContainer).hide()
		this._scrollDown();
		//$(parent).find("." + this._default.finishSequenceFixedClass).hide();
	},
	
	_showSelectedPlugin : function(selectedDataCollection,context) {
		var self = this;
		var info = null;
		if (selectedDataCollection) {
			info = this._appMenuHandler._getSelectedDbInfoUsingDataCollection(selectedDataCollection);
		}
		var parent = $(context).closest("." + this._default.appContainerClass);
		var method = $(parent).find("." + self._default.selectMethodList).val();
		var analysisMethod = $(parent).find("." + self._default.analysisMethodComboClass).val();
		$container = $(parent).find("." + self._default.actionResultContainer);
		$container.html("Loading...");
		//$(parent).find("." + this._default.applicationOptionClass).hide();
		$(parent).find("." + this._default.nextButtonContainerClass).hide();
		var date = new Date();
		var id = "container_id_" + date.getTime();
		//var appOption = $(parent).find("." + self._default.applicationOptionClass + " input[name=applicationOption]:checked").val();
		var fixedSeq = $("#" + self._default.baseSequenceContainerId + " ." + self._default.fixedSequenceClass).html();
		$container.attr("id", id);
		var func = function() {
			self._callback(parent, self);
		}
		var obj = {
			workId : (info) ? info.workId : "",
			fileName : (info) ? info.fileName : "",
			rankListWorkId : (info) ? info.rankListWorkId : "",
			plotingWorkId : (info) ? info.plotingWorkId : "",
			baseSequence : self._baseSequence,
			tooltip : self._tooltip,
			callback : func,
			//applicationOption : appOption,
			fixedSequence : fixedSeq,
			motifMethod : this._getSelectedAnalysisMethod(parent),
			dataColl : selectedDataCollection,
			analysisMethod : analysisMethod
		};
		
		eval(method)(id, obj);
		self._scrollDown();
	},
	
	_fillAnalysisMethodCombo : function(selectToolCmbRef) {
		var parent = $(selectToolCmbRef).closest("." + this._default.appContainerClass);
		var selectedTool = $(selectToolCmbRef).val();
		var analysisMethods = this._appMenuHandler._getFilteredDistinctAnalysisMethods(selectedTool);
		var analysisMethodCmb = $(parent).find("." + this._default.analysisMethodComboClass);
		this._fillCombo(analysisMethods, analysisMethodCmb, this._default.analysisMethodComboEmptyOptionText, this._tooltipName.analysisMethod);
	},
	
	_fillExpressionDBCombo : function(analysisMethodCmbRef) {
		var parent = $(analysisMethodCmbRef).closest("." + this._default.appContainerClass);
		var selectedTool = this._getSelectedTool(parent);
		var selectedAnalysisMethod = $(analysisMethodCmbRef).val();
		var expressionDbs = this._appMenuHandler._getFilteredDistinctExpressionDbs(selectedTool,selectedAnalysisMethod);
		var analysisMethodCmb = $(parent).find("." + this._default.expressionDbComboClass);
		this._fillCombo(expressionDbs, analysisMethodCmb, this._default.expressionDbComboEmptyOptionText, this._tooltipName.expressionDb);
	},
	
	_fillDataCollectionCombo : function(expressionDbRef) {
		var parent = $(expressionDbRef).closest("." + this._default.appContainerClass);
		var selectedTool = this._getSelectedTool(parent);
		var selectedAnalysisMethod = this._getSelectedAnalysisMethod(parent);
		var selectedExpressionDb = $(expressionDbRef).val();
		var dataCollections = this._appMenuHandler._getFilteredDistinctDataCollections(selectedTool,selectedAnalysisMethod,selectedExpressionDb);
		var dataColCmb = $(parent).find("." + this._default.dataColomboClass);
		this._fillCombo(dataCollections, dataColCmb, this._default.dataColColomboEmptyOptionText, this._tooltipName.dataCollection);
	},
		
	_fillCombo : function(optionsArr, cmbRef, firstOptionText, firstOptionToolTipKey) {
		$(cmbRef).empty();
		var toolTip = this._tooltip.getByKey(firstOptionToolTipKey);
		$(cmbRef).append("<option value='-1' title='"+ toolTip +"'>"+ firstOptionText +"</option>");
		for (var index = 0 ; index < optionsArr.length ; index++) {
			var option = optionsArr[index];
			toolTip = this._tooltip.getByKey(option);
			$(cmbRef).append("<option value='"+ option + "' title='"+ toolTip +"'>"+ option +"</option>");
		}	
	},

_fillEmptyBaseSequence : function() {
		var self = this, sb = [];
		for (var i = 0; i < self._default.baseSequenceMaxLength; i++) {
			sb[sb.length] = self.CHAR_SEQ_EMPTY;
		}
		$baseInput = $("#" + this._default.baseSequenceContainerId + " ." + this._default.baseSequenceClass);
		$baseInput.val(sb.join(""));
	},
	
	_loadPluginScriptList : function(workId, fileName, property) {
		var getTripleList = function(tripleList) {
			$.each(tripleList, function(tKey, tVal) {
				LinkDataUtil.loadScript(tVal.object);
			});
		}
		LinkData.getTriplesByProperty(workId, fileName, property, getTripleList);
	},
	
	_changeMethodList : function(dbKey) {
		var self = this;
		var $select = $("." + self._default.appContainerClass + " ." + self._default.selectMethodList);
		$select.attr("title", self._getToolTip(self._tooltipName.selectTool));
		$("option", $select).remove();
		$select.append("<option value='-1' selected='selected'>-- Select Tool --</option>");
		if (dbKey == -1) {
			return;
		}
		var arr = dbKey.split("|");
		var workId = arr[0];
		var fileName = arr[1];
		$.each(self._methodList, function(key, method) {
			self._addValidMethod($select, workId, fileName, method);
		});
	},
	
	_addValidMethod : function($select, workId, fileName, method) {
		var self = this;
		var getFilesByTag = function(fileList) {
			if (!fileList) {
				return;
			}
			$.each(fileList, function(fKey, fName) {
				if (fName === fileName) {
					var tooltip = self._getToolTipByToolName(method);
					tooltip = (tooltip) ? tooltip : "";
					$select.append("<option value='" + method + "' title='" + tooltip + "'>" + method + "</option>");
					return false;
				}
			});
		}
		LinkData.getFilesByTag(workId, method, getFilesByTag);
	},
	
	_initUseButtonListener : function() {
		var self = this;
		$("#" + self._default.baseSequenceContainerId + " ." + self._default.useButtonClass).click(function() {
			self._initDefaultContainer();
			$txtSeq = $("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass);
			$fixedSeq = $("#" + self._default.baseSequenceContainerId + " ." + self._default.fixedSequenceClass);
			self._hideError();
			if ($txtSeq.val().length > self._default.baseSequenceMaxLength) {
				self._showError(self._default.errorMessageMaximumSequence.replace("{0}", self._default.baseSequenceMaxLength));
				return;
			}
			self._showWarningForNonStandardCharsIfExists();
			if ($txtSeq.val().length < self._default.baseSequenceMaxLength) {
				var tmpVal = $txtSeq.val();
				var eVal = self._getExtraDefaultSequence(self._default.baseSequenceMaxLength - $txtSeq.val().length);
				$txtSeq.val(eVal + tmpVal);
				$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass).attr("size", 500);
			}
			self._baseSequence = $txtSeq.val().toString().toLowerCase() + $fixedSeq.html();
			if (!self._baseSequence || self._baseSequence.length < self._default.baseSequenceMinLength) {
				self._showError(self._default.errorMessageEnterSequence.replace("{0}", self._default.baseSequenceMinLength));
			} else {
				//$txtSeq.attr('readonly', true).addClass("noborder");
				$(this).hide();
				$("." + self._default.appContainerClass).show();
				$("." + self._default.appContainerClass + " ." + self._default.expressionDbContainer).hide();
		    	$("." + self._default.appContainerClass + " ." + self._default.dataColContainer).hide();
				$("." + self._default.appContainerClass + " ." + self._default.analysisMethodContainer).hide();
				$("." + self._default.appContainerClass + " ." + self._default.nextButtonContainerClass).hide();
				$("." + self._default.appContainerClass + " ." + self._default.finishSequenceContainer).hide()
			}
		});
	},
	
	_showWarningForNonStandardCharsIfExists : function() {
		var found = false;
		var txtSeq = $("#" + this._default.baseSequenceContainerId + " ." + this._default.baseSequenceClass).val();
		for (var i = 0 ; i < txtSeq.length ; i++) {
			var char = txtSeq.charAt(i).toString().toUpperCase();
			if (this._validCharcters.indexOf(char) == -1) {
				$("div." + this._default.baseSequenceErrDivClass).show();
				found = true;
				break;
			}
		}
		if (found == false) {
			$("div." + this._default.baseSequenceErrDivClass).hide();
		}
	},
	
	_callback : function(parent, self) {
		if (self._isSelectedManualMotif(parent)) {
			$("." + self._default.appContainerClass + " ." + self._default.finishNowButtonClass).hide();
			$("." + self._default.appContainerClass + " ." + self._default.repeatButtonClass).hide();
			//self._initNextButtonListener();
		} else {
			$("." + self._default.appContainerClass + " ." + self._default.finishNowButtonClass).show();
			$("." + self._default.appContainerClass + " ." + self._default.finishNowButtonClass).attr("title", self._getToolTip(self._tooltipName.finishNow));
			$("." + self._default.appContainerClass + " ." + self._default.repeatButtonClass).show();
			self._initFinishNowButtonListener();
		}
		$(parent).find("." + self._default.nextButtonContainerClass).show();
		$(parent).find("." + self._default.finishSequenceContainer).hide();
		$("." + self._default.appContainerClass + " ." + self._default.nextButtonClass).attr("title", self._getToolTip(self._tooltipName.next));
		$(parent).find("." + self._default.nextButtonContainerClass).show();
		self._initNextButtonListener();
		self._initRepeatButtonListner();
	},
	
	_isSelectedManualMotif : function(parent) {
		var toolCombo = $(parent).find("." + this._default.selectMethodList);
		var selectedTool = toolCombo.val();
		if (selectedTool == this._default.manualMotifEntryToolName) {
			return true;
		} else {
			return false;
		}
	},
	
	_initNextButtonListener : function() {
		var self = this;
		$("." + self._default.appContainerClass + " ." + self._default.nextButtonClass).unbind('click');
		$("." + self._default.appContainerClass + " ." + self._default.nextButtonClass).click(function() {
			$parent = $(this).closest("." + self._default.appContainerClass);
			$parent.find("." + self._default.nextButtonContainerClass).hide();
			$($parent).find("." + self._default.finishSequenceContainer).hide()
			var clone = $parent.clone(true);
			//$(clone).find("." + self._default.applicationOptionClass).hide();
			var text = $(clone).find(".replaceSequence").text();
			if (text && text.trim().length != 0) {
				self._baseSequence = text;
			}
			$(clone).find("." + self._default.actionResultContainer).html("");
			$(clone).find("." + self._default.nextButtonContainerClass).hide();
			$(clone).find("." + self._default.expressionDbContainer).hide();
		    $(clone).find(" ." + self._default.dataColContainer).hide();
			$(clone).find(" ." + self._default.analysisMethodContainer).hide();
			$parent.parent().append(clone);
			self._scrollDown();
		});
	},
	
	_initFinishNowButtonListener : function() {
		var self = this;
		$("." + self._default.appContainerClass + " ." + self._default.finishNowButtonClass).unbind('click');
		$("." + self._default.appContainerClass + " ." + self._default.finishNowButtonClass).click(function() {
			var parent = $(this).closest("." + self._default.appContainerClass);
			$(parent).find("." + self._default.nextButtonContainerClass).hide();
			$(parent).find("." + self._default.finishSequenceContainer).hide()
			var gene = $(parent).find(".replaceSequence .gene").val();
			var geneType = $(parent).find(".replaceSequence .geneType").val();
			if (gene && geneType) {
				var callback = function(bSequence) {
					self._showFinishedBaseSequence(parent, bSequence);
				}
				//self._appBaseLineSequence.getBaseSequence(gene, geneType, callback);
				self._appBaseLineSequence._getBaseSequence(gene, callback);
			} else {
				self._showFinishedBaseSequence(parent,self._baseSequence);
			}
			self._scrollDown();
		});
	},
	
	_initRepeatButtonListner : function() {
		var self = this;
		$("." + self._default.appContainerClass + " ." + self._default.repeatButtonClass).unbind('click');
		$("." + self._default.appContainerClass + " ." + self._default.repeatButtonClass).click(function() {
			$parent = $(this).closest("." + self._default.appContainerClass);
			$parent.find("." + self._default.nextButtonContainerClass).hide();
			$($parent).find("." + self._default.finishSequenceContainer).hide()
			var clone = $parent.clone(true);
			var text = $(clone).find(".replaceSequence").text();
			if (text && text.trim().length != 0) {
				self._baseSequence = text;
			}
			$(clone).find("." + self._default.actionResultContainer).html("");
			$(clone).find("." + self._default.nextButtonContainerClass).hide();
			// setting the values
			var tool = $($parent).find("." + self._default.selectMethodList).val();	
			var expressionDb = $($parent).find("." + self._default.expressionDbComboClass).val();
			//var dataCollection = $($parent).find("." + self._default.dataColomboClass).val();
			var analysisMethod = $($parent).find("." + self._default.analysisMethodComboClass).val();
			$(clone).find("." + self._default.selectMethodList).val(tool);
			$(clone).find("." + self._default.expressionDbComboClass).val(expressionDb);
		    //$(clone).find(" ." + self._default.dataColomboClass).val(dataCollection);
			$(clone).find(" ." + self._default.analysisMethodComboClass).val(analysisMethod);
			$parent.parent().append(clone);
			self._scrollDown();
		});
	},
	
	_showFinishedBaseSequence : function(parent, bSequence) {
		var self = this;
		var defaultSequence = $(parent).find(".replaceSequence").text()
		$(parent).find(".wrappedSequenceMotif").hide();	
		var html = self._getFinishedBaseSequence(defaultSequence, bSequence);
		var fixedSequence = self._getFixedSequence();
		$(parent).find("." + self._default.finishSequenceContainer).show();
		$(parent).find("." + self._default.finishSequenceFixedClass).html(fixedSequence);
		//$(parent).find("." + self._default.finishSequenceFixedClass).show();
		$(parent).find("." + self._default.finishSequence).html(html);
		$(parent).find("." + self._default.finishSequence).scrollLeft(10000);
	},
	
	_getFixedSequence : function() {
		var fixedSequence = $("#" + this._default.baseSequenceContainerId + " ." + this._default.fixedSequenceClass).html();
		return fixedSequence;
	},
	
	_getFinishedBaseSequence : function(defaultSequence, bSequence) {
		var self = this, sb = [];
		var fixedSequence = this._getFixedSequence();
		var uptoFixedSequence = defaultSequence.length - fixedSequence.length;
		for (var i = 0; i < defaultSequence.length; i++) {
			if (i > uptoFixedSequence - 1) {
				continue;
			}
			var dChar = defaultSequence.charAt(i);
			var bChar = bSequence.charAt(i);
			if (bChar) {
				if (dChar !== self.CHAR_SEQ_EMPTY) {
					sb[sb.length] = "<span class='highlight-sequence'><span class='replace'>" + dChar + "</span></span>";
				} else {
					sb[sb.length] = bChar.toLowerCase();
				}
			} else {
				sb[sb.length] = "<span class='highlight-sequence'><span class='replace'>" + dChar + "</span></span>";
			}
		}
		return sb.join("");
	},
	
	_getExtraDefaultSequence : function(count) {
		var self = this, sb = [];
		for (var i = 0; i < count; i++) {
			sb[sb.length] = self.CHAR_SEQ_EMPTY;
		}
		return sb.join("");
	},
	
	_getDatabaseOptionKey : function(workId, fileName) {
		return workId + "|" + fileName;
	},
	
	_getLabel : function(value) {
		var propLabel = value;
		var arr = value.split("#");
		if (arr.length > 1) {
			propLabel = decodeURIComponent(arr[1]);
		}
		return propLabel;
	},
	
	_showError : function(message) {
		var self = this;
		$errMsgEl = $("#" + self._default.baseSequenceContainerId + " ." + self._default.baseErrorMessageClass);
		$errMsgEl.html(message);
		$errMsgEl.show();
	},
	
	_hideError : function() {
		var self = this;
		$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseErrorMessageClass).hide();
	},
	
	_getToolTipByFileName : function(fileName) {
		var self = this;
		if (fileName) {
			if (fileName.toLowerCase().indexOf(self._tooltipName.atGeneExpress) > -1) {
				return self._getToolTip(self._tooltipName.atGeneExpress);
			} else if (fileName.toLowerCase().indexOf(self._tooltipName.diunal) > -1) {
				return self._getToolTip(self._tooltipName.diunal);
			}
		}
	},
	
	_getToolTipByToolName : function(tool) {
		var self = this;
		if (tool) {
			if (tool.toLowerCase().indexOf(self._tooltipName.motifExpress) > -1) {
				return self._getToolTip(self._tooltipName.motifExpress);
			} else if (tool.toLowerCase().indexOf(self._tooltipName.motifCircatian) > -1) {
				return self._getToolTip(self._tooltipName.motifCircatian);
			} else if (tool.toLowerCase().indexOf(self._tooltipName.motifRank) > -1) {
				return self._getToolTip(self._tooltipName.motifRank);
			} else if (tool.toLowerCase().indexOf(self._tooltipName.motifQuery) > -1) {
				return self._getToolTip(self._tooltipName.motifQuery);
			} else if (tool.toLowerCase().indexOf(self._tooltipName.inputMotif) > -1) {
				return self._getToolTip(self._tooltipName.inputMotif);
			}
		}
	},
	
	_getToolTip : function(key) {
		return this._tooltip.getByKey(key);
	}
	
};

Application.MenuHandler = function() {
	this._init.apply(this,arguments);
}

Application.MenuHandler.prototype = {
	
	_fullList : [],
	_currentFilteredList : [],
	_workId : null,
	_fileName : null,
	_fileProperties : null,
	
	_properties : {
		motifAnalysisMethod : "motif%20analysis%20method",
		geneExpressionData : "gene%20expression%20data",
		menuDisplayName : "menu%20display%20name",
		toolsList : "tool%20list",
		workIdInTest : "test.linkdata.org",
		workIdPublic : "linkdata.org",
		ranklistWorkIdTest : "rank%20list%20test.linkdata.org",
		ranklistWorkIdPublic : "rank%20list%20linkdata.org",
		plotingDataWorkIdTest :"plot%20in%20test.linkdata.org",
		plotingDataWorkIdPublic :"plot%20in%20linkdata.org"
    },
	
	_tags : {
		menuDataSourceTag : "menu"
	},
	
	_defaults : {
		linkdataTestUrl : "test.linkdata.org",
		linkdataPublicUrl : "linkdata.org",
	},
	
	_init : function(args) {
		this._initMenuDataSource();
	},
	
	_fillFileProperties : function() {
		var self = this;
		var setProperties = function(props) {
			self._fileProperties = props;
		};
		LinkData.getProperties(this._workId,this._fileName,setProperties);
	},
	
	_initMenuDataSource : function() {
		var self = this;
		var foundMenuFiles = [];
		var loadMenuFiles = function(resultList) {
			$.each(resultList, function(wId, fileList) {
				$.each(fileList, function(fileKey, fName) {
					var obj = {
						workId : wId,
						fileName : fName
					};
					foundMenuFiles.push(obj);
				});
			});
			self._foundMenuFiles = foundMenuFiles;
			self._loadMenuFileContent(foundMenuFiles);
			self._fillFileProperties();
		};
		LinkData.getFilesByTag(null, this._tags.menuDataSourceTag, loadMenuFiles);
	},
	
	_loadMenuFileContent : function(menuFiles) {
		var self = this;
		var addFileContent = function(triples) {
			for (var index = 0 ; index < triples.length ; index++) {
				self._fullList.push(triples[index]);
			}
		};
		if (menuFiles.length > 1) {
			alert("There can be only one file that can be tagged with 'menu'");
			return;
		}
		if (menuFiles.length == 0) {
			return;
		}
		var obj = menuFiles.shift(); // removing the first element
		this._fileName = obj.fileName;
		this._workId = obj.workId;
		LinkData.getTriples(this._workId,this._fileName,addFileContent,{start:1, end:2000});
	},
	
	
	_getFilteredAnalysisMethodTriples : function(toolName) {
		if (!(toolName)) return this._fullList;
		this._currentFilteredList = [];
		var listByTool = this._getTriplesByProperty(this._properties.toolsList,this._fullList);
		if (!listByTool) return null;
		var filteredList = [];
		for (var index = 0 ; index < listByTool.length ; index++) {
			var triple = listByTool[index];
			if (triple.object) {
				var toolList = triple.object.split(",");
				for (var index1 = 0 ; index1 < toolList.length ; index1++) {
					var tool = toolList[index1];
					if (tool.trim() == toolName.trim()) {
						var subject = triple.subject;
						var otherPropTripleList = this._getTriplesBySubject(subject);
						for (var index1 = 0 ; index1 < otherPropTripleList.length ; index1++) {
							var propTriple = otherPropTripleList[index1];
							//this._currentFilteredList.push(propTriple);
							filteredList.push(propTriple);
						}
						break;
					}
				}
			}
		}
	    return filteredList;
	},
	
	_getFilteredDistinctAnalysisMethods : function(toolName) {
		var filteredList = this._getFilteredAnalysisMethodTriples(toolName);
		this._currentFilteredList = filteredList;
		var distinctList = this._getDistinctObjectList(this._properties.motifAnalysisMethod,filteredList);
		return distinctList;
	},
		
	_getFilteredExpressionDbTriples : function(toolName,analysisMethodName) {
		var listByTool = this._getFilteredAnalysisMethodTriples(toolName);
		var listByAnalysisMethod = this._getTriplesByProperty(this._properties.motifAnalysisMethod,listByTool);
		if (!listByAnalysisMethod) return null;
		var filteredList = [];
		for (var index = 0 ; index < listByAnalysisMethod.length ; index++) {
			var triple = listByAnalysisMethod[index];
			if (triple.object) {
				var analysisMethod = triple.object;
				if (analysisMethod.trim() == analysisMethodName.trim()) {
					var subject = triple.subject;
					var otherPropTripleList = this._getTriplesBySubject(subject);
					for (var index1 = 0 ; index1 < otherPropTripleList.length ; index1++) {
						var propTriple = otherPropTripleList[index1];
						//this._currentFilteredList.push(propTriple);
						filteredList.push(propTriple);
					}
				}
			}
		}
		return filteredList
	},
	
	_getFilteredDistinctExpressionDbs : function(toolName,analysisMethodName) {
		var filteredList = this._getFilteredExpressionDbTriples(toolName,analysisMethodName);
		this._currentFilteredList = filteredList;
		var distinctList = this._getDistinctObjectList(this._properties.geneExpressionData,filteredList);
		return distinctList;
	},
		
	_getFilteredDataCollectionTriples : function(toolName,analysisMethodName,expressionDbName) {
		var listByExpDbs = this._getFilteredExpressionDbTriples(toolName,analysisMethodName);
		var listByGeneExp = this._getTriplesByProperty(this._properties.geneExpressionData,listByExpDbs);
		if (!listByGeneExp) return null;
		var filteredList = [];
		for (var index = 0 ; index < listByGeneExp.length ; index++) {
			var triple = listByGeneExp[index];
			if (triple.object) {
				var exprssionDb = triple.object;
				if (exprssionDb.trim() == expressionDbName.trim()) {
					var subject = triple.subject;
					var otherPropTripleList = this._getTriplesBySubject(subject);
					for (var index1 = 0 ; index1 < otherPropTripleList.length ; index1++) {
						var propTriple = otherPropTripleList[index1];
						//this._currentFilteredList.push(propTriple);
						filteredList.push(propTriple);
					}
				}
			}
		}
		return filteredList;
	},
		
	_getFilteredDistinctDataCollections : function(toolName,analysisMethodName,expressionDbName) {
		var filteredList = this._getFilteredDataCollectionTriples(toolName,analysisMethodName,expressionDbName);
		this._currentFilteredList = filteredList;
		var distinctList = this._getDistinctObjectList(this._properties.menuDisplayName,filteredList);
		return distinctList;
	},
	
	_getSelectedDbInfoUsingDataCollection : function(dataCollectionName) {
		var matchingList = [];
		var outObj = null;
		var listByDataCollection = this._getTriplesByProperty(this._properties.menuDisplayName,this._currentFilteredList);
		if (!listByDataCollection) return null;
		for (var index = 0 ; index < listByDataCollection.length ; index++) {
			var triple = listByDataCollection[index];
			var dataCollection = triple.object;
			if (dataCollection == dataCollectionName) {
				matchingList.push(triple);
			}
		}
		if (matchingList.length > 1) {
			// this a error. because there can be only one matching triple
			alert("Data file error");
		} else {
			// getting other triples for found one
			var subject = matchingList.shift().subject;
			var workId, rankWorkId, plotingWorkId = null;
			var otherPropTripleList = this._getTriplesBySubject(subject);
			var workIdProperty = this._getWorkIdProperty();
			var rankWorkIdProp = this._getRankingWorkIdProperty();
			var plotingWorkIdProp = this._getPlotingWorkIdProperty();
			for (var index=0 ; index < otherPropTripleList.length ; index++) {
				var triple = otherPropTripleList[index];
				var prop = this._getProperty(triple.property);
				if (workIdProperty == prop) {
					workId = triple.object;
				}
				if (rankWorkIdProp == prop) {
					rankWorkId = triple.object;
				}
				if (plotingWorkIdProp == prop) {
					plotingWorkId = triple.object;
				}
				if (workId && rankWorkId && plotingWorkId) {
					break;
				}
			}
			var workIdComps = workId.split("/");
			var rankWorkIdComps = rankWorkId.split("/");
			var plotingWorkIdComps = plotingWorkId.split("/");
			var subjectComps = subject.split("#");
			outObj = {
				fileName : subjectComps[subjectComps.length-1],
				workId : workIdComps[workIdComps.length-1],
				rankListWorkId : rankWorkIdComps[rankWorkIdComps.length-1],
				plotingWorkId : plotingWorkIdComps[plotingWorkIdComps.length-1]
			};
		}
		return outObj;
	},
	
	_getProperty : function(propertyUrl) {
		var comps = propertyUrl.split("#");
		return comps[comps.length-1];
	},
	
	_getWorkIdProperty : function() {
		var hostName = window.location.hostname;
		if (hostName.indexOf(this._defaults.linkdataTestUrl) != -1) {
			return this._properties.workIdInTest;
		} else if (hostName.indexOf(this._defaults.linkdataPublicUrl) != -1) {
			return this._properties.workIdPublic;
		}
	},
	
	_getRankingWorkIdProperty : function() {
		var hostName = window.location.hostname;
		if (hostName.indexOf(this._defaults.linkdataTestUrl) != -1) {
			return this._properties.ranklistWorkIdTest;
		} else if (hostName.indexOf(this._defaults.linkdataPublicUrl) != -1) {
			return this._properties.ranklistWorkIdPublic;
		}
	},
	
	_getPlotingWorkIdProperty : function() {
		var hostName = window.location.hostname;
		if (hostName.indexOf(this._defaults.linkdataTestUrl) != -1) {
			return this._properties.plotingDataWorkIdTest;
		} else if (hostName.indexOf(this._defaults.linkdataPublicUrl) != -1) {
			return this._properties.plotingDataWorkIdPublic;
		}
	},
	
	_getTriplesByProperty : function(propName,currentList) {
		/*
          this function first will find the triple with the passed property and then
		  this will take the subject of it and will find other properties of that
          subject
		*/
		var filteredList = [];
		//var currentList = this._getCurrentUsingList();
		for (var index = 0 ; index < currentList.length ; index++) {
			var triple = currentList[index];
			var prop = this._getProperty(triple.property);
			if (prop == propName) {
				filteredList.push(triple);
			}
		}
		return filteredList;
	},
	
	_getTriplesBySubject : function(subject) {
		var filteredList = [];
		var currentList = this._getCurrentUsingList();
		for (var index = 0 ; index < currentList.length ; index++) {
			var triple = currentList[index];
			var triSubject = triple.subject;
			if (triSubject.trim() == subject.trim()) {
				filteredList.push(triple);
			}
			if (filteredList.length == this._fileProperties.length) {
				break;
			}
		}
		return filteredList;
	},
	
	// returns a string array
	_getDistinctObjectList : function(propName,currentList) {
		var distinctList = [];
		for (var index = 0 ; index < currentList.length ; index++) {
			var triple = currentList[index];
			var prop = triple.property;
			if (prop && prop.indexOf(propName) != -1) {
				var objVal = triple.object;
				if (distinctList.indexOf(objVal) == -1) {
					distinctList.push(objVal);
				}
			}
		}
		return distinctList;
	},
	
	_getCurrentUsingList : function() {
		if (this._currentFilteredList.length == 0) {
			return this._fullList;
		} else {
			return this._currentFilteredList;
		}
	},
}
/*	
Application.baseLineSequence = function() {
	this._init.apply(this, arguments);
};

Application.baseLineSequence.prototype = {
	
	_attedSequenceInfo : null,
	_ppdbSequenceInfo : null,
	
	_default : {
		sequenceProperty : "baseline%20sequence"
	},
	
	_tag : {
		attedBaseSequenceTag : "atted_baseLineSequence",
		ppdbBaseSequenceTag : "ppdb_baseLineSequence"
	},
	
	_init : function() {
		this._attedSequenceInfo = {};
		this._ppdbSequenceInfo = {};
		this._initBaseSequenceFile();
	},
	
	_initBaseSequenceFile : function() {
		this._initAttedBaseSequenceFile();
		this._initPpdbBaseSequenceFile();
	},
	
	_initAttedBaseSequenceFile : function() {
		var self = this;
		var getFilesByTag = function(resultList) {
			$.each(resultList, function(workId, fileList) {
				$.each(fileList, function(fileKey, fileName) {
					self._initAttedInfo(workId, fileName);
					return false;
				});
			});
		}
		LinkData.getFilesByTag(null, self._tag.attedBaseSequenceTag, getFilesByTag);
	},
	
	_initPpdbBaseSequenceFile : function() {
		var self = this;
		var getFilesByTag = function(resultList) {
			$.each(resultList, function(workId, fileList) {
				$.each(fileList, function(fileKey, fileName) {
					self._initPpdbInfo(workId, fileName);
					return false;
				});
			});
		}
		LinkData.getFilesByTag(null, self._tag.ppdbBaseSequenceTag, getFilesByTag);
	},
	
	_initAttedInfo : function(workId, fileName) {
		var self = this;
		var getProperties = function(propertyList) {
			$.each(propertyList, function(pKey, pValue) {
				var propOnly = pValue.split("#")[1];
				if (propOnly == self._default.sequenceProperty) {
					self._attedSequenceInfo.workId = workId;
					self._attedSequenceInfo.fileName = fileName;
					self._attedSequenceInfo.property = pValue;
					return false;
				}
			});
		}
		LinkData.getProperties(workId, fileName, getProperties);
	},
	
	_initPpdbInfo : function(workId, fileName) {
		var self = this;
		var getProperties = function(propertyList) {
			$.each(propertyList, function(pKey, pValue) {
				var propOnly = pValue.split("#")[1];
				if (propOnly == self._default.sequenceProperty) {
					self._ppdbSequenceInfo.workId = workId;
					self._ppdbSequenceInfo.fileName = fileName;
					self._ppdbSequenceInfo.property = pValue;
					return false;
				}
			});
		}
		LinkData.getProperties(workId, fileName, getProperties);
	},
	
	_getAttedSubjectUrl : function(gene) {
		return "http://atted.jp/data/locus/" + gene + ".html";
	},
	
	_getPpdbSubjectUrl : function(gene) {
		return "http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/display.cgi?organism=At&gene=" + gene;
	},
	
	_getAttedBaseSequence : function(gene, callback) {
		var self = this;
		var workId = self._attedSequenceInfo.workId;
		var fileName = self._attedSequenceInfo.fileName;
		var property = self._attedSequenceInfo.property;
		var subject = self._getAttedSubjectUrl(gene);
		var getObjects = function(objList) {
			callback(objList[0]);
		}
		LinkData.getObjects(workId, fileName, subject, property, getObjects);
	},
	
	_getPpdbBaseSequence : function(gene, callback) {
		var self = this;
		var workId = self._ppdbSequenceInfo.workId;
		var fileName = self._ppdbSequenceInfo.fileName;
		var property = self._ppdbSequenceInfo.property;
		var subject = self._getPpdbSubjectUrl(gene);
		var getObjects = function(objList) {
			callback(objList[0]);
		}
		LinkData.getObjects(workId, fileName, subject, property, getObjects);
	},
	
	getBaseSequence : function(gene, geneType, callback) {
		var self = this;
		if ("ATTED" === geneType) {
			self._getAttedBaseSequence(gene, callback);
		} else if ("PPDB" === geneType) {
			self._getPpdbBaseSequence(gene, callback);
		} else {
			// error
		}
	}
};
*/
Application.baseLineSequence = function() {
	this._init.apply(this,arguments);
}
	
Application.baseLineSequence.prototype = {
	
	_baseLineSeqFileInfo : null,
	
	_default : {
		sequenceProperty : "promoter%20sequence",
		linkdataTestUrl : "test.linkdata.org",
		linkdatapublicUrl : "linkdata.org"
	},
	
	_tag : {
		baseSequenceTag : "promoter_sequence",
	},
	
	_init : function() {
		this._findBaseLineSequenceFile();
		this._baseLineSeqFileInfo = {};
	},
	
	_findBaseLineSequenceFile : function() {
		// looking one tagged file only
		var self = this;
		var getFilesByTag = function(resultList) {
			$.each(resultList, function(workId, fileList) {
				$.each(fileList, function(fileKey, fileName) {
					self._initBaseLineSequenceFileInfo(workId, fileName);
					return false;
				});
			});
		}
		LinkData.getFilesByTag(null, self._tag.baseSequenceTag, getFilesByTag);
	},
	
	_initBaseLineSequenceFileInfo : function(workId, fileName) {
		var self = this;
		var getProperties = function(propertyList) {
			$.each(propertyList, function(pKey, pValue) {
				var propOnly = pValue.split("#")[1];
				if (propOnly == self._default.sequenceProperty) {
					self._baseLineSeqFileInfo.workId = workId;
					self._baseLineSeqFileInfo.fileName = fileName;
					self._baseLineSeqFileInfo.property = pValue;
					return false;
				}
			});
		};
		LinkData.getProperties(workId, fileName, getProperties);
	},
	
	_getSubject : function(gene) {
		var hostName = window.location.hostname;
		var subject = null;
		gene = gene.toUpperCase();
		if (hostName.indexOf(this._default.linkdataTestUrl) != -1) {
			subject = this._default.linkdataTestUrl + "/resource/" + this._baseLineSeqFileInfo.workId + "#" + gene;
		} else if (hostName.indexOf(this._default.linkdatapublicUrl) != -1) {
			subject = this._default.linkdatapublicUrl + "/resource/" + this._baseLineSeqFileInfo.workId + "#" + gene;;
		}
		return "http://" + subject;
	},
	
	_getBaseSequence : function(gene, callback) {
		var self = this;
		var workId = self._baseLineSeqFileInfo.workId;
		var fileName = self._baseLineSeqFileInfo.fileName;
		var property = self._baseLineSeqFileInfo.property;
		var subject = self._getSubject(gene);
		var getObjects = function(objList) {
			callback(objList[0]);
		}
		LinkData.getObjects(workId, fileName, subject, property, getObjects);
	}
}

Application.tooltip = function() {
	this._init.apply(this, arguments);
};

Application.tooltip.prototype = {
	
	_toolTipList : null,
	
	_default : {
		explanationProperty : "explanation"
	},
	
	_init : function() {
		this._toolTipList = [];
		this._initToolTip();
	},
	
	_initToolTip : function() {
		var self = this;
		var getFilesByTag = function(resultList) {
			$.each(resultList, function(workId, fileList) {
				$.each(fileList, function(fileKey, fileName) {
					self._getFilePropertyList(workId, fileName);
				});
			});
		}
		LinkData.getFilesByTag(null, "tooltip", getFilesByTag);
	},
	
	_getFilePropertyList : function(workId, fileName) {
		var self = this;
		var index = new Application.index(1, 10000);
		var getProperties = function(propertyList) {
			$.each(propertyList, function(pKey, pValue) {
				if (pValue.indexOf(self._default.explanationProperty) > -1) {
					self._getSubjectList(workId, fileName, pValue, index);
					return false;
				}
			});
		}
		LinkData.getProperties(workId, fileName, getProperties);
	},
	
	_getSubjectList : function(workId, fileName, property, index) {
		var self = this;
		var getSubjects = function(subjectList) {
			self._getPropertyList(subjectList, workId, fileName, property, index);
		}
		LinkData.getSubjects(workId, fileName, getSubjects, index);
	},
	
	_getPropertyList : function(subjectList, workId, fileName, property, index) {
		var self = this;
		var getTriplesByProperty = function(tripleList) {
			self._addToolTipToList(subjectList, tripleList, workId, fileName, property, index);
		}
		LinkData.getTriplesByProperty(workId, fileName, property, getTriplesByProperty, index);
	},
	
	_addToolTipToList : function(subjectList, tripleList, workId, fileName, property, index) {
		var self = this;
		for (var i = 0; i < subjectList.length; i++) {
			var key = self._getLabelAfterHash(subjectList[i]);
			if (tripleList[i]) {
				var value = tripleList[i].object;
				self._addToolTip(key, value);
			}
		}
		if (subjectList && subjectList.length == index.getItemCount()) {
			self._getSubjectList(workId, fileName, property, index.increment());
		}
	},
	
	_addToolTip : function(key, tooltip) {
		var obj = {};
		obj.key = key;
		obj.tooltip = tooltip;
		this._toolTipList.push(obj);
	},
	
	getByKey : function(key) {
		var self = this, tooltip;
		$.each(self._toolTipList, function(objKey, obj) {
			if (obj.key.toString().toLowerCase() === key.toString().toLowerCase()) {
				tooltip = obj.tooltip;
				return false;
			}
		});
		return (tooltip) ? tooltip : "";
	},
	
	_getLabelAfterHash : function(value) {
		var propLabel = value;
		var arr = value.split("#");
		if (arr.length > 1) {
			propLabel = decodeURIComponent(arr[1]);
		}
		return propLabel;
	}
};

Application.index = function() {
	this._init.apply(this, arguments);
}

Application.index.prototype = {
	
	_start : null,
	_end : null,
	
	_init : function(start, end) {
		this._start = start;
		this._end = end;
	},
	
	getIndex : function() {
		return {start : this._start, end : this._end};
	},
	
	getItemCount : function() {
		return (this._end - this._start + 1);
	},
	
	increment : function() {
		var itemCount = this.getItemCount();
		this._start = this._start + itemCount;
		this._end = this._end + itemCount;
		return {start : this._start, end : this._end};
	},
	
	getStartIndex : function() {
		return this._start;
	},
	
	getEndIndex : function() {
		return this._end;
	}
	
};

Application.timer = function() {
	this._init.apply(this, arguments);
};

Application.timer.prototype = {
	
	_delay : null,
	_retry : null,
	_maxRetry : null,
	
	_init : function() {
		this._delay = 1000;
		this._retry = 0;
		this._maxRetry = 100;
	},
	
	call : function(func) {
		if (this._retry < this._maxRetry) {
			setTimeout(func, this._delay);
		}
		this._retry++;
	},
	
	setMaxRetryCount : function(no) {
		this._maxRetry = no;
	}
};

Application.MotifConflication = function() {
	this._init.apply(this, arguments);
};

$(document).ready(function() {
	new Application.genocon();
});

body {
    font-family: sans-serif;
    font-size: 14px;
}

a {
    color: #3B5998;
    font-weight: bold;
    text-decoration: none;
}

#gcAppContainer {
	width: 900px;
}

.hidden {
	display:none;
}

.left {
    float: left;
}

.label {
	color: #E87B10;
    font: 1.1em "Trebuchet MS","Helvetica","Arial","Verdana","sans-serif";
    height: 24px;
    min-width: 165px;
}

input.baseSequence {
	/*width: 100%;*/
}

.highlight-sequence {
	font-weight: bold;
}

.resultArea {
    font-family: "Courier New","Lucida Console";
    margin: 10px 0;
    min-width: 410px;
    overflow: auto;
    width: 100%;
	background-color: #FFFFFF;
    border: 1px solid #DDDDDD;
	white-space: nowrap;
}

.resultArea .userSequence {
	white-space: nowrap;
	float: left;
}

.finishSequence,
.replaceSequenc {
   background-color: #FFFFFF;
    border: 1px solid #DDDDDD;
    margin: 10px 0 0;
	font-family: "Courier New","Lucida Console";
	width: 100%;
	overflow: auto;
	white-space: nowrap;
}

.wrappedSequenceMotif {
	background-color: #FFFFFF;
    border: 1px solid #DDDDDD;
    margin: 10px 0 0;
	font-family: "Courier New","Lucida Console";
	overflow: auto;
	word-wrap: break-word;
	white-space: normal;
	width:100%;
	height:90px;
	word-break: break-all;
}

.replace {
    color: #E80010;
}

.baseErrorMessage,
.errorMessage {
	color: black;
	/*text-align: center;*/
	margin-bottom: -10px;
    margin-top: 10px;
}

.errorText {
	color: #FF0000;
}

.applicationContainer {
    background-color: #F6F6F6;
    border: 1px solid #CCCCCC;
    margin: 5px 0 0;
    padding: 5px;
}

.actionButtonContainer {
    text-align: right;
}

.actionBtn {
    border: 1px solid #DDDDDD;
    cursor: pointer;
    display: inline-block;
    font-weight: bold;
    padding: 5px 2px;
    text-align: center;
    width: 25px;
}

.row {
    padding: 5px 0;
}
.row:after {
    clear: left;
    content: "";
    display: block;
}
.row input[type="text"] {
    width: 200px;
}

.row .externalLink {
	margin: 0 5px;
}

.noborder {
    border: medium none;
}

#baseSequenceContainer .baseSequenceBox {
	width: 100%;
	overflow: auto;
	white-space: nowrap;
}
#baseSequenceContainer .baseSequenceBox span,
#baseSequenceContainer .baseSequenceBox .baseSequence {
	font-family: Courier;
}

#baseSequenceContainer .baseSequenceBox .fixedSequence {
	position: relative;
	left: -6px;
	color: #AAAAAA;
	font-weight: bold;
}

.applicationContainer .nextButtonContainer {
	margin-top: 10px;
}

.databaseInfo .motif {
	width: 70%;
}

/**
 * button css
 */

a.useButton {
	width: 150px;
}

.actionBtn {
	border: 1px solid #DDDDDD;
    cursor: pointer;
    display: inline-block;
    font-weight: bold;
    padding: 5px 2px;
    text-align: center;
    width: 25px;
}

.actionBtn:hover {
	border: 1px solid #000000;
}

.btn {
  display: inline-block;
  *display: inline;
  /* IE7 inline-block hack */

*zoom: 1;
  padding: 4px 10px 4px;
  margin-bottom: 0;
  font-size: 13px;
  line-height: 18px;
  color: #333333;
  text-align: center;
  text-shadow: 0 1px 1px rgba(255, 255, 255, 0.75);
  vertical-align: middle;
  background-color: #f5f5f5;
  background-image: -moz-linear-gradient(top, #ffffff, #e6e6e6);
  background-image: -ms-linear-gradient(top, #ffffff, #e6e6e6);
  background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));
  background-image: -webkit-linear-gradient(top, #ffffff, #e6e6e6);
  background-image: -o-linear-gradient(top, #ffffff, #e6e6e6);
  background-image: linear-gradient(top, #ffffff, #e6e6e6);
  background-repeat: repeat-x;
  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);
  border-color: #e6e6e6 #e6e6e6 #bfbfbf;
  border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
  filter: progid:dximagetransform.microsoft.gradient(enabled=false);
  border: 1px solid #cccccc;
  border-bottom-color: #b3b3b3;
  -webkit-border-radius: 4px;
  -moz-border-radius: 4px;
  border-radius: 4px;
  -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
  -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
  box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
  cursor: pointer;
  *margin-left: .3em;
}

.btn:hover,
.btn:active,
.btn.active,
.btn.disabled,
.btn[disabled] {
  background-color: #e6e6e6;
}

.btn:hover {
  color: #333333;
  text-decoration: none;
  background-color: #e6e6e6;
  background-position: 0 -15px;
  -webkit-transition: background-position 0.1s linear;
  -moz-transition: background-position 0.1s linear;
  -ms-transition: background-position 0.1s linear;
  -o-transition: background-position 0.1s linear;
  transition: background-position 0.1s linear;
}

.btn-blue,
.btn-blue:hover,
.btn-yellow,
.btn-yellow:hover,
.btn-red,
.btn-red:hover,
.btn-green,
.btn-green:hover,
.btn-lightblue,
.btn-lightblue:hover,
.btn-black,
.btn-black:hover {
  text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
  color: #ffffff;
}

.btn-blue {
  background-color: #0074cc;
  background-image: -moz-linear-gradient(top, #0088cc, #0055cc);
  background-image: -ms-linear-gradient(top, #0088cc, #0055cc);
  background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#0088cc), to(#0055cc));
  background-image: -webkit-linear-gradient(top, #0088cc, #0055cc);
  background-image: -o-linear-gradient(top, #0088cc, #0055cc);
  background-image: linear-gradient(top, #0088cc, #0055cc);
  background-repeat: repeat-x;
  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#0088cc', endColorstr='#0055cc', GradientType=0);
  border-color: #0055cc #0055cc #003580;
  border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
  filter: progid:dximagetransform.microsoft.gradient(enabled=false);
}

.btn-blue:hover,
.btn-blue:active,
.btn-blue.active,
.btn-blue.disabled,
.btn-blue[disabled] {
  background-color: #0055cc;
}

.btn-green {
  background-color: #5bb75b;
  background-image: -moz-linear-gradient(top, #62c462, #51a351);
  background-image: -ms-linear-gradient(top, #62c462, #51a351);
  background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#51a351));
  background-image: -webkit-linear-gradient(top, #62c462, #51a351);
  background-image: -o-linear-gradient(top, #62c462, #51a351);
  background-image: linear-gradient(top, #62c462, #51a351);
  background-repeat: repeat-x;
  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#62c462', endColorstr='#51a351', GradientType=0);
  border-color: #51a351 #51a351 #387038;
  border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
  filter: progid:dximagetransform.microsoft.gradient(enabled=false);
}
.btn-green:hover,
.btn-green:active,
.btn-green.active,
.btn-green.disabled,
.btn-green[disabled] {
  background-color: #51a351;
}
.btn-green:active,
.btn-green.active {
  background-color: #408140 ¥9;
}
.btn-lightblue {
  background-color: #49afcd;
  background-image: -moz-linear-gradient(top, #5bc0de, #2f96b4);
  background-image: -ms-linear-gradient(top, #5bc0de, #2f96b4);
  background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#2f96b4));
  background-image: -webkit-linear-gradient(top, #5bc0de, #2f96b4);
  background-image: -o-linear-gradient(top, #5bc0de, #2f96b4);
  background-image: linear-gradient(top, #5bc0de, #2f96b4);
  background-repeat: repeat-x;
  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#5bc0de', endColorstr='#2f96b4', GradientType=0);
  border-color: #2f96b4 #2f96b4 #1f6377;
  border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
  filter: progid:dximagetransform.microsoft.gradient(enabled=false);
}
.btn-lightblue:hover,
.btn-lightblue:active,
.btn-lightblue.active,
.btn-lightblue.disabled,
.btn-lightblue[disabled] {
  background-color: #2f96b4;
}

/* Dialog css */

.motifViewDialog .explanation {
	color: #AAAAAA;
	font-size: 12px;
	margin-left: 200px;
	margin-top : -10px;
}

.motifViewDialog .moreInfo {
	color: #3B5998;
	cursor: pointer;
}

.motifViewDialog .position {
	width: 70px;
}

.motifViewDialog .dialogErrorMessage {
	font-size: 12px;
}

.ui-corner-all, .ui-corner-top, .ui-corner-left, .ui-corner-tl {
    border-top-left-radius: 1px;
}
.ui-corner-all, .ui-corner-top, .ui-corner-right, .ui-corner-tr {
    border-top-right-radius: 1px;
}
.ui-corner-all, .ui-corner-bottom, .ui-corner-left, .ui-corner-bl {
    border-bottom-left-radius: 1px;
}
.ui-corner-all, .ui-corner-bottom, .ui-corner-right, .ui-corner-br {
    border-bottom-right-radius: 1px;
}

.loadingImageContainer .loadingMessage {
	color: #FF0000;
}

.motifConflictionDialog .option {
	margin: 10px;
}

.motifViewDialog {
	margin-top: 10px;	
}

.motifViewDialog .label {
	color: #E87B10;
    font: 1.1em "Trebuchet MS","Helvetica","Arial","Verdana","sans-serif";
    height: 24px;
    width : 200px;
}

.motifViewDialog .motifviewinfo {
	float: right;
    margin-top: -150px;
    position: relative;
    width: 350px;	
}

.deletelink {
	cursor: pointer;	
}

.deletelink img {
	margin-bottom: -3px;	
}

.manualMotifView .manualMotifViewInfo {
	float: right;
    height: 90px;
    margin-right: 10px;
    margin-top: -65px;
    position: relative;
    width: 380px;
}

.baseSequenceBox textarea {
	resize: none;	
	width: 490px;
	height: 115px;
}

.fixedSequenceCheckBox {
	float: right;
    margin-right: 210px;
    margin-top: -115px;
}

.fixedSequenceMsg {
	float: right;
    margin-right: 20px;
    margin-top: -40px;
}

.fixedSequenceMotif {
	display: inline;
    float: right;
    font-family: "Courier New","Lucida Console";
    margin-top: -15px;
}

.resultAreaUserMessageClass {
	color: #0A5DA6;
    font: bold 1.1em "Trebuchet MS","Helvetica","Arial","Verdana","sans-serif";
    font-size: 12px;
    font-weight: bold;
    margin-top: -6px;
	margin-bottom: 4px;
}

.finishSequence {
	 background-color: #FFFFFF;
    border: 1px solid #DDDDDD;
    font-family: "Courier New","Lucida Console";
    height: 100px;
    margin: 10px 0 0;
    overflow: auto;
    width: 480px;
    word-break: break-all;
    word-wrap: break-word;
	white-space: normal;
}

.finishSequenceFixed {
	/*display: inline;
    float: right;
    font-family: "Courier New","Lucida Console";
    margin-top: -15px;*/
	display: inline;
    float: left;
    font-family: "Courier New","Lucida Console";
    margin-left: 488px;
    margin-top: -30px;
    overflow: auto;
    width: 400px;
	word-wrap: break-word;
}

.manualsequence {
	float: right;
    height: 40px;
    overflow: auto;
    width: 300px;
	margin-bottom: 5px;
}

.motifviewsequence {
	float: right;
    height: 40px;
    margin-bottom: 5px;
    overflow: auto;
    width: 240px;
}

div.warningTop {
	background-color:#F6F6F6;
	font-weight:bold;
	color:#223194;
}

.error {
	color:#ED4A68;
}

.loadingChart .loadChartMessage {
	color:#FF0000;
}

.loadingChart {
	text-align: center;
}

.bottomChartTitle {
    color: #0A5DA6;
    font: bold 12px "Trebuchet MS","Helvetica","Arial","Verdana","sans-serif";
}

.finishSequenceMsg {
	color: #0A5DA6;
    float: right;
    font: bold 13px "Trebuchet MS","Helvetica","Arial","Verdana","sans-serif";
    margin-top: -80px;
    width: 400px;
}

<div id="tests"> </div>
<div class="warningTop">Hover mouse over menu items for tooltip descriptions</div>
</br>
<div id="gcAppContainer">

<div id="baseSequenceContainer">
	<div class="label baseSequenceLabel">Base Sequence</div>
	<div class="baseSequenceBox">
		<span>
			<textarea type="text" cols=45 rows=5 class="baseSequence" value="" disabled=true maxlength=500> </textarea>
		</span>
		
		<span class="fixedSequence">GATCCCAAGACCCTTCCTCTATATAAGGAAGTTCATTTCATTTGGAGAGG</span>
		
		<div>
			<div class="fixedSequenceCheckBox"><input type="checkbox" id="chkEmptySequnce" value="true" checked=true>Start with empty sequence</div>
			<div class="fixedSequenceMsg">Minimal Promoter (fixed)</div>
		</div>
	</div>
	<div style="margin-top:5px;"><a class="useButton btn btn-green">Start promoter design</a></div>
	<div class="baseErrorMessage hidden"></div>
</div>
<div class="baseSequenceError hidden error">
	Warning: Motif contains nonstandard characters for DNA design. All characters except A, T, C, G will be treated as unique special characters. Currently IUPAC codes are not supported.
</div>
<div class="applicationContainer hidden">
	<div class="actionButtonContainer">
		<span class="appSummery"></span>
		<span class="collapseButton actionBtn" title="collapse">_</span>
		<span class="expandButton actionBtn" title="expand">+</span>
		<span class="removeButton actionBtn" title="remove">x</span>
		<br clear="all"/>
	</div>
	<div class="applicationDataContainer">
		
		<div class="row">
			<div class="label left optionListLabel">Select Tool</div>
			<div class="left">
				<select class="optionList"></select>
				
			</div>
		</div>

<div class="row hidden analysisMethodContainer">
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Circadian Genomic (DIURNAL + PPDB promoter motif) normalized Contributor:Koro_Nishikata Update:May 10, 2013 951 Downloads, 10 Applications Normalized Expression Data of DIURNAL circadian conditions, combined with LDSS sequence analysis of regulatory (8mer) motif calculations (PPDB). <br><br> <strong>References</strong> (for PPDB):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17947329">http://www.ncbi.nlm.nih.gov/pubmed/17947329</a><br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17346352">http://www.ncbi.nlm.nih.gov/pubmed/17346352</a> <br> <strong>References</strong> (for DIURNAL)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18419293">http://www.ncbi.nlm.nih.gov/pubmed/18419293</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_COL_LDHH_normalize.html#work_information'>DiurnalHours_PPDB_COL_LDHH_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_COL_SD_normalize.html#work_information'>DiurnalHours_PPDB_COL_SD_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_DD_DDHC_normalize.html#work_information'>DiurnalHours_PPDB_DD_DDHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Dark (12h) Dark (12h) / Hot (12h) / Cold (12h), and subjected to Dark (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_LDHC_normalize.html#work_information'>DiurnalHours_PPDB_LDHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (12h) / Cold (12h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_LDHH_SM_normalize.html#work_information'>DiurnalHours_PPDB_LDHH_SM_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h), by using the Smith method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_LDHH_ST_normalize.html#work_information'>DiurnalHours_PPDB_LDHH_ST_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h), by using the Stitt method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_LER_SD_normalize.html#work_information'>DiurnalHours_PPDB_LER_SD_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler (Landsberg-ereta) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_LIGHT5_HIF138_13_normalize.html#work_information'>DiurnalHours_PPDB_LIGHT5_HIF138_13_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis hif138-13 (HETEROGENOUS INBRED FAMILY 138-13) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_LIGHT5_HIF138_8_normalize.html#work_information'>DiurnalHours_PPDB_LIGHT5_HIF138_8_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis hif138-8 (HETEROGENOUS INBRED FAMILY 138-8) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_LIGHT5_znknOX_normalize.html#work_information'>DiurnalHours_PPDB_LIGHT5_znknOX_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis tsp-ox (hif138-8) (TANDEM ZINCKNUCKLE PROTEIN-ox) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_LL12_LDHH_normalize.html#work_information'>DiurnalHours_PPDB_LL12_LDHH_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (24h), and subjected to Light (24h) by the Kay method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_LL23_LDHH_normalize.html#work_information'>DiurnalHours_PPDB_LL23_LDHH_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (24h), and subjected to Light (24h) by the Miller method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_LLHC_normalize.html#work_information'>DiurnalHours_PPDB_LLHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (12h) / Cold (12h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_LL_LDHC_normalize.html#work_information'>DiurnalHours_PPDB_LL_LDHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (12h) / Cold (12h), and subjected to Light (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_LL_LLHC_normalize.html#work_information'>DiurnalHours_PPDB_LL_LLHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (12h) / Cold (12h), and subjected to Light (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_lhyox_SD_normalize.html#work_information'>DiurnalHours_PPDB_lhyox_SD_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis lhy (lhy-ox) (LATE ELONGATED HYPOCOTYL) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_longday_normalize.html#work_information'>DiurnalHours_PPDB_longday_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler strain, grown under the circadian condition of long day light, that is, Light (16h) Dark (8h) by using the Kay method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_lux_2_LDHH_normalize.html#work_information'>DiurnalHours_PPDB_lux_2_LDHH_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis lux-2 (LUX ARRHYTHMO-2) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_phyB9_SD_normalize.html#work_information'>DiurnalHours_PPDB_phyB9_SD_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis phyB9 (PHYTOCHROME B-9) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s708i/DiurnalHours_PPDB_shortday_normalize.html#work_information'>DiurnalHours_PPDB_shortday_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h) by using the Kay method. </td> </tr> </table> <br> <br> <b> <a name="license" style="color:#666666"> License </a> </b> <br> <p> We would like to thank Dr. Yoshiharu Yamamoto for supplying the data of PPDB (Plant Promoter Database) for <a href="http://promotercad.org">PromoterCAD</a> & <a href="http://genocon.org">GenoCon2</a> competition. License of this work's data is according to the intentions of the PPDB original data source.</a> <br> <a href="http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi">http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi</a> </p>	DiurnalHours_PPDB_COL_LDHH_normalize DiurnalHours_PPDB_COL_SD_normalize DiurnalHours_PPDB_DD_DDHC_normalize DiurnalHours_PPDB_LDHC_normalize DiurnalHours_PPDB_LDHH_SM_normalize DiurnalHours_PPDB_LDHH_ST_normalize DiurnalHours_PPDB_LER_SD_normalize DiurnalHours_PPDB_LIGHT5_HIF138_13_normalize DiurnalHours_PPDB_LIGHT5_HIF138_8_normalize DiurnalHours_PPDB_LIGHT5_znknOX_normalize DiurnalHours_PPDB_LL12_LDHH_normalize DiurnalHours_PPDB_LL23_LDHH_normalize DiurnalHours_PPDB_LLHC_normalize DiurnalHours_PPDB_LL_LDHC_normalize DiurnalHours_PPDB_LL_LLHC_normalize DiurnalHours_PPDB_lhyox_SD_normalize DiurnalHours_PPDB_longday_normalize DiurnalHours_PPDB_lux_2_LDHH_normalize DiurnalHours_PPDB_phyB9_SD_normalize DiurnalHours_PPDB_shortday_normalize
PromoterCAD Data Tables Contributor:GenoCon Update:May 16, 2013 60 Downloads, 6 Applications This will allow the PromoteCAD Application to find the appropriate tools, the input data and the gene rank list.	PromoterCAD_Data_Tables [menu]
Rank Lists of Diurnal PPDB Contributor:Koro_Nishikata Update:May 10, 2013 151 Downloads, 14 Applications Lists for the expression of Diurnal and PPDB mashup data table. For each experiment, all genes ranked by circadian amplitude. <br><br> <strong>References</strong> (for PPDB):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17947329">http://www.ncbi.nlm.nih.gov/pubmed/17947329</a><br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17346352">http://www.ncbi.nlm.nih.gov/pubmed/17346352</a><br> <strong>References</strong> (for Diurnal)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18419293">http://www.ncbi.nlm.nih.gov/pubmed/18419293</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s713i/DiurnalHours_PPDB_all.html#work_information'>DiurnalHours PPDB all</a> </td> <td> Lists for the DIURNAL and PPDB mashup data table. For each experiment, the all genes ranked by expression level. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s713i/DiurnalHours_PPDB_GeneRank_for_MotifCircadian_all.html#work_information'>DiurnalHours PPDB GeneRank for MotifCircadian all</a> </td> <td> Lists for the DIURNAL and PPDB (Plant Promoter Database) mashup data table. For each experiment, the all genes ranked by circadian amplitude. </td> </tr> </table> <br> <br> <b> <a name="license" style="color:#666666"> License </a> </b> <br> <p> We would like to thank Dr. Yoshiharu Yamamoto for supplying the data of PPDB (Plant Promoter Database) for <a href="http://promotercad.org">PromoterCAD</a> & <a href="http://genocon.org">GenoCon2</a> competition. License of this work's data is according to the intentions of the PPDB original data source.</a> <br> <a href="http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi">http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi</a> </p>	DiurnalHours_PPDB_GeneRank_for_MotifCircadian_all [motifcircadian] DiurnalHours_PPDB_all [motifexpress]
Rank Lists of AtGenExpress mean gene expression + PLACE promoter motif Contributor:Koro_Nishikata Update:Apr 29, 2013 32 Downloads, 5 Applications Lists for the AtGenExpress and PLACE mashup data table. For each experiment, all genes ranked by absolute level of mean expression. <br><br> <strong>References</strong> (for PLACE)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/9847208">http://www.ncbi.nlm.nih.gov/pubmed/9847208</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s775i/AtGenExpress_PLACE_mean_all.html#work_information'>AtGenExpress_PLACE_mean_all</a> </td> <td> Lists for the AtGenExpress and PLACE mashup data table. For each experiment, all genes ranked by absolute level of mean expression. </td> </tr> </table>	AtGenExpress_PLACE_mean_all [motifexpress]
Developmental Genomic (AtGenExpress Developmental gene expression + PPDB promoter motif) Triplicate Data Contributor:Koro_Nishikata Update:May 10, 2013 302 Downloads, 7 Applications Full triplicate expression dataset of AtGenExpress plant developmental tissues, combined with LDSS sequence analysis of regulatory (8mer) motif calculations (PPDB). MotifExpress tool allows the plloting of all triplicate data points during the design process, so the user has some idea of the experimental variation in the measurements. <br><br> <strong>References</strong> (for PPDB):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17947329">http://www.ncbi.nlm.nih.gov/pubmed/17947329</a><br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17346352">http://www.ncbi.nlm.nih.gov/pubmed/17346352</a> <br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s782i/AtGenExpress_PPDB_Flowering.html#work_information'>AtGenExpress_PPDB_Flowering</a> </td> <td> This collection of Gene Expression Properties are associated with flowering tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s782i/AtGenExpress_PPDB_Fruit_Seeds.html#work_information'>AtGenExpress_PPDB_Fruit_Seeds</a> </td> <td> <br> This collection of Gene Expression Properties are associated with fruit and seed tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s782i/AtGenExpress_PPDB_Leaf.html#work_information'>AtGenExpress_PPDB_Leaf</a> </td> <td> <br> This collection of Gene Expression Properties are associated with leaf tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s782i/AtGenExpress_PPDB_Root.html#work_information'>AtGenExpress_PPDB_Root</a> </td> <td> <br> This collection of Gene Expression Properties are associated with root tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s782i/AtGenExpress_PPDB_Seedling.html#work_information'>AtGenExpress_PPDB_Seedling</a> </td> <td> <br> This collection of Gene Expression Properties are associated with seedling tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s782i/AtGenExpress_PPDB_Stem.html#work_information'>AtGenExpress_PPDB_Stem</a> </td> <td> <br> This collection of Gene Expression Properties are associated with stem tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s782i/AtGenExpress_PPDB_Whole_Plant.html#work_information'>AtGenExpress_PPDB_Whole_Plant</a> </td> <td> <br> This collection of Gene Expression Properties are associated with whole plant body parts. </td> </tr> </table> <br> <br> <b> <a name="license" style="color:#666666"> License </a> </b> <br> <p> We would like to thank Dr. Yoshiharu Yamamoto for supplying the data of PPDB (Plant Promoter Database) for <a href="http://promotercad.org">PromoterCAD</a> & <a href="http://genocon.org">GenoCon2</a> competition. License of this work's data is according to the intentions of the PPDB original data source.</a> <br> <a href="http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi">http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi</a> </p>	AtGenExpress_PPDB_Flowering AtGenExpress_PPDB_Fruit_Seeds AtGenExpress_PPDB_Leaf AtGenExpress_PPDB_Root AtGenExpress_PPDB_Seedling AtGenExpress_PPDB_Stem AtGenExpress_PPDB_Whole_Plant
DIURNAL normalized gene expression + PLACE promoter motif Contributor:Koro_Nishikata Update:Apr 29, 2013 757 Downloads, 6 Applications Normalized Expression Data of DIURNAL circadian conditions, combined with PLACE (Plant Cis-acting Regulatory DNA Elements) motif database. <br><br> <strong>References</strong> (for PLACE):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/9847208">http://www.ncbi.nlm.nih.gov/pubmed/9847208</a><br> <strong>References</strong> (for DIURNAL)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18419293">http://www.ncbi.nlm.nih.gov/pubmed/18419293</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_COL_LDHH_normalize.html#work_information'>DiurnalHours_PLACE_COL_LDHH_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_COL_SD_normalize.html#work_information'>DiurnalHours_PLACE_COL_SD_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_DD_DDHC_normalize.html#work_information'>DiurnalHours_PLACE_DD_DDHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Dark (12h) Dark (12h) / Hot (12h) / Cold (12h), and subjected to Dark (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_LDHC_normalize.html#work_information'>DiurnalHours_PLACE_LDHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (12h) / Cold (12h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_LDHH_SM_normalize.html#work_information'>DiurnalHours_PLACE_LDHH_SM_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h), by using the Smith method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_LDHH_ST_normalize.html#work_information'>DiurnalHours_PLACE_LDHH_ST_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h), by using the Stitt method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_LER_SD_normalize.html#work_information'>DiurnalHours_PLACE_LER_SD_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler (Landsberg-ereta) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_LIGHT5_HIF138_13_normalize.html#work_information'>DiurnalHours_PLACE_LIGHT5_HIF138_13_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis hif138-13 (HETEROGENOUS INBRED FAMILY 138-13) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_LIGHT5_HIF138_8_normalize.html#work_information'>DiurnalHours_PLACE_LIGHT5_HIF138_8_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis hif138-8 (HETEROGENOUS INBRED FAMILY 138-8) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_LIGHT5_znknOX_normalize.html#work_information'>DiurnalHours_PLACE_LIGHT5_znknOX_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis tsp-ox (hif138-8) (TANDEM ZINCKNUCKLE PROTEIN-ox) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_LL12_LDHH_normalize.html#work_information'>DiurnalHours_PLACE_LL12_LDHH_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (24h), and subjected to Light (24h) by the Kay method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_LL23_LDHH_normalize.html#work_information'>DiurnalHours_PLACE_LL23_LDHH_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (24h), and subjected to Light (24h) by the Miller method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_LLHC_normalize.html#work_information'>DiurnalHours_PLACE_LLHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (12h) / Cold (12h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_LL_LDHC_normalize.html#work_information'>DiurnalHours_PLACE_LL_LDHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (12h) / Cold (12h), and subjected to Light (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_LL_LLHC_normalize.html#work_information'>DiurnalHours_PLACE_LL_LLHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (12h) / Cold (12h), and subjected to Light (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_lhyox_SD_normalize.html#work_information'>DiurnalHours_PLACE_lhyox_SD_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis lhy (lhy-ox) (LATE ELONGATED HYPOCOTYL) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_longday_normalize.html#work_information'>DiurnalHours_PLACE_longday_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler strain, grown under the circadian condition of long day light, that is, Light (16h) Dark (8h) by using the Kay method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_lux_2_LDHH_normalize.html#work_information'>DiurnalHours_PLACE_lux_2_LDHH_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis lux-2 (LUX ARRHYTHMO-2) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_phyB9_SD_normalize.html#work_information'>DiurnalHours_PLACE_phyB9_SD_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis phyB9 (PHYTOCHROME B-9) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s747i/DiurnalHours_PLACE_shortday_normalize.html#work_information'>DiurnalHours_PLACE_shortday_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h) by using the Kay method. </td> </tr> </table>	DiurnalHours_PLACE_COL_LDHH_normalize DiurnalHours_PLACE_COL_SD_normalize DiurnalHours_PLACE_DD_DDHC_normalize DiurnalHours_PLACE_LDHC_normalize DiurnalHours_PLACE_LDHH_SM_normalize DiurnalHours_PLACE_LDHH_ST_normalize DiurnalHours_PLACE_LER_SD_normalize DiurnalHours_PLACE_LIGHT5_HIF138_13_normalize DiurnalHours_PLACE_LIGHT5_HIF138_8_normalize DiurnalHours_PLACE_LIGHT5_znknOX_normalize DiurnalHours_PLACE_LL12_LDHH_normalize DiurnalHours_PLACE_LL23_LDHH_normalize DiurnalHours_PLACE_LLHC_normalize DiurnalHours_PLACE_LL_LDHC_normalize DiurnalHours_PLACE_LL_LLHC_normalize DiurnalHours_PLACE_lhyox_SD_normalize DiurnalHours_PLACE_longday_normalize DiurnalHours_PLACE_lux_2_LDHH_normalize DiurnalHours_PLACE_phyB9_SD_normalize DiurnalHours_PLACE_shortday_normalize
Developmental Coexpression (AtGenExpress + ATTED-II promoter motif) normalized Contributor:Koro_Nishikata Update:Apr 22, 2013 277 Downloads, 10 Applications Normalized Expression Data of AtGenExpress plant developmental tissues, combined with CEG coexpression analysis regulatory (7mer) motif calculations (ATTED-II). <br><br> <strong>References</strong> (for ATTED-II):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17130150">http://www.ncbi.nlm.nih.gov/pubmed/17130150</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s585i/AtGenExpress_ATTED_Flowering_normalize.html#work_information'>AtGenExpress_ATTED_Flowering_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with flowering tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s585i/AtGenExpress_ATTED_Fruit_Seeds_normalize.html#work_information'>AtGenExpress_ATTED_Fruit_Seeds_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with fruit and seed tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s585i/AtGenExpress_ATTED_Leaf_normalize.html#work_information'>AtGenExpress_ATTED_Leaf_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with leaf tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s585i/AtGenExpress_ATTED_Root_normalize.html#work_information'>AtGenExpress_ATTED_Root_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with root tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s585i/AtGenExpress_ATTED_Seedling_normalize.html#work_information'>AtGenExpress_ATTED_Seedling_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with seedling tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s585i/AtGenExpress_ATTED_Stem_normalize.html#work_information'>AtGenExpress_ATTED_Stem_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with stem tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s585i/AtGenExpress_ATTED_Whole_Plant_normalize.html#work_information'>AtGenExpress_ATTED_Whole_Plant_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with whole plant body parts. </td> </tr> </table>	AtGenExpress_ATTED_Flowering_normalize AtGenExpress_ATTED_Fruit_Seeds_normalize AtGenExpress_ATTED_Leaf_normalize AtGenExpress_ATTED_Root_normalize AtGenExpress_ATTED_Seedling_normalize AtGenExpress_ATTED_Stem_normalize AtGenExpress_ATTED_Whole_Plant_normalize
Developmental Coexpression (AtGenExpress + ATTED-II promoter motif) mean Contributor:Koro_Nishikata Update:Apr 25, 2013 333 Downloads, 5 Applications Developmental Microarray Expression Data (AtGenExpress) of plant developmental tissues, combined with CEG coexpression analysis regulatory (7mer) motif calculations (ATTED-II). We took the mean of triplicate measurements from AtGenExpress, then sorted the developmental series into plant organs (Flower, Leaf, Root, Stem, Fruit & Seeds), with one category for seedlings (8 days old or less) and another for whole plants (older than 8 days). Gene Loci without expression data or motif data were removed from this database. <br><br> <strong>References</strong> (for ATTED-II):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17130150">http://www.ncbi.nlm.nih.gov/pubmed/17130150</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s769i/AtGenExpress_ATTED_Flowering_mean.html#work_information'>AtGenExpress_ATTED_Flowering_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with flowering tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s769i/AtGenExpress_ATTED_Fruit_Seeds_mean.html#work_information'>AtGenExpress_ATTED_Fruit_Seeds_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with fruit and seed tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s769i/AtGenExpress_ATTED_Leaf_mean.html#work_information'>AtGenExpress_ATTED_Leaf_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with leaf tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s769i/AtGenExpress_ATTED_Root_mean.html#work_information'>AtGenExpress_ATTED_Root_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with root tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s769i/AtGenExpress_ATTED_Seedling_mean.html#work_information'>AtGenExpress_ATTED_Seedling_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with seedling tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s769i/AtGenExpress_ATTED_Stem_mean.html#work_information'>AtGenExpress_ATTED_Stem_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with stem tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s769i/AtGenExpress_ATTED_Whole_Plant_mean.html#work_information'>AtGenExpress_ATTED_Whole_Plant_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with whole plant body parts. </td> </tr> </table> . </td> </tr> </table>	AtGenExpress_ATTED_Flowering_mean AtGenExpress_ATTED_Fruit_Seeds_mean AtGenExpress_ATTED_Leaf_mean AtGenExpress_ATTED_Root_mean AtGenExpress_ATTED_Seedling_mean AtGenExpress_ATTED_Stem_mean AtGenExpress_ATTED_Whole_Plant_mean
PromoterCAD plugin tools Contributor:GenoCon Update:May 16, 2013 53 Downloads, 4 Applications This file is used to register new plugin tools for use in forked versions of PromoterCAD.	PromoterCAD_plugins [method]
Developmental Genomic (AtGenExpress + PPDB promoter motif) mean Contributor:Koro_Nishikata Update:May 10, 2013 282 Downloads, 5 Applications Developmental Microarray Expression Data (AtGenExpress) of plant developmental tissues, combined with LDSS sequence analysis of regulatory (8mer) motif calculations (PPDB). We took the mean of triplicate measurements from AtGenExpress, then sorted the developmental series into plant organs (Flower, Leaf, Root, Stem, Fruit & Seeds), with one category for seedlings (8 days old or less) and another for whole plants (older than 8 days). For each motif, we calculated the position relative to the TSS as determined experimentally (PPDB). Gene Loci without expression data or motif data were removed from this database. <br><br> <strong>References</strong> (for PPDB):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17947329">http://www.ncbi.nlm.nih.gov/pubmed/17947329</a><br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17346352">http://www.ncbi.nlm.nih.gov/pubmed/17346352</a> <br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s778i/AtGenExpress_PPDB_Flowering_mean.html#work_information'>AtGenExpress_PPDB_Flowering_mean</a> </td> <td> This collection of Gene Expression Properties are associated with flowering tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s778i/AtGenExpress_PPDB_Fruit_Seeds_mean.html#work_information'>AtGenExpress_PPDB_Fruit_Seeds_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with fruit and seed tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s778i/AtGenExpress_PPDB_Leaf_mean.html#work_information'>AtGenExpress_PPDB_Leaf_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with leaf tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s778i/AtGenExpress_PPDB_Root_mean.html#work_information'>AtGenExpress_PPDB_Root_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with root tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s778i/AtGenExpress_PPDB_Seedling_mean.html#work_information'>AtGenExpress_PPDB_Seedling_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with seedling tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s778i/AtGenExpress_PPDB_Stem_mean.html#work_information'>AtGenExpress_PPDB_Stem_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with stem tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s778i/AtGenExpress_PPDB_Whole_Plant_mean.html#work_information'>AtGenExpress_PPDB_Whole_Plant_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with whole plant body parts. </td> </tr> </table> <br> <br> <b> <a name="license" style="color:#666666"> License </a> </b> <br> <p> We would like to thank Dr. Yoshiharu Yamamoto for supplying the data of PPDB (Plant Promoter Database) for <a href="http://promotercad.org">PromoterCAD</a> & <a href="http://genocon.org">GenoCon2</a> competition. License of this work's data is according to the intentions of the PPDB original data source.</a> <br> <a href="http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi">http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi</a> </p>	AtGenExpress_PPDB_Flowering_mean AtGenExpress_PPDB_Fruit_Seeds_mean AtGenExpress_PPDB_Leaf_mean AtGenExpress_PPDB_Root_mean AtGenExpress_PPDB_Seedling_mean AtGenExpress_PPDB_Stem_mean AtGenExpress_PPDB_Whole_Plant_mean
Developmental Genomic (AtGenExpress + PPDB promoter motif) normalized Contributor:Koro_Nishikata Update:May 10, 2013 302 Downloads, 10 Applications Normalized Expression Data of AtGenExpress plant developmental tissues, combined with LDSS sequence analysis of regulatory (8mer) motif calculations (PPDB). <br> <br> <strong>References</strong> (for PPDB):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17947329">http://www.ncbi.nlm.nih.gov/pubmed/17947329</a><br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17346352">http://www.ncbi.nlm.nih.gov/pubmed/17346352</a> <br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s707i/AtGenExpress_PPDB_Flowering_normalize.html#work_information'>AtGenExpress_PPDB_Flowering_normalize</a> </td> <td> This collection of Gene Expression Properties are associated with flowering tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s707i/AtGenExpress_PPDB_Fruit_Seeds_normalize.html#work_information'>AtGenExpress_PPDB_Fruit_Seeds_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with fruit and seed tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s707i/AtGenExpress_PPDB_Leaf_normalize.html#work_information'>AtGenExpress_PPDB_Leaf_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with leaf tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s707i/AtGenExpress_PPDB_Root_normalize.html#work_information'>AtGenExpress_PPDB_Root_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with root tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s707i/AtGenExpress_PPDB_Seedling_normalize.html#work_information'>AtGenExpress_PPDB_Seedling_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with seedling tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s707i/AtGenExpress_PPDB_Stem_normalize.html#work_information'>AtGenExpress_PPDB_Stem_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with stem tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s707i/AtGenExpress_PPDB_Whole_Plant_normalize.html#work_information'>AtGenExpress_PPDB_Whole_Plant_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with whole plant body parts. </td> </tr> </table> <br> <br> <b> <a name="license" style="color:#666666"> License </a> </b> <br> <p> We would like to thank Dr. Yoshiharu Yamamoto for supplying the data of PPDB (Plant Promoter Database) for <a href="http://promotercad.org">PromoterCAD</a> & <a href="http://genocon.org">GenoCon2</a> competition. License of this work's data is according to the intentions of the PPDB original data source.</a> <br> <a href="http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi">http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi</a> </p>	AtGenExpress_PPDB_Flowering_normalize AtGenExpress_PPDB_Fruit_Seeds_normalize AtGenExpress_PPDB_Leaf_normalize AtGenExpress_PPDB_Root_normalize AtGenExpress_PPDB_Seedling_normalize AtGenExpress_PPDB_Stem_normalize AtGenExpress_PPDB_Whole_Plant_normalize
AtGenExpress normalized gene expression + PLACE promoter motif Contributor:Koro_Nishikata Update:Apr 29, 2013 348 Downloads, 6 Applications Normalized Expression Data of AtGenExpress plant developmental tissues, combined with PLACE (Plant Cis-acting Regulatory DNA Elements) motif database. <br><br> <strong>References</strong> (for PLACE)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/9847208">http://www.ncbi.nlm.nih.gov/pubmed/9847208</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s741i/AtGenExpress_PLACE_Flowering_normalize.html#work_information'>AtGenExpress_PLACE_Flowering_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with flowering tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s741i/AtGenExpress_PLACE_Fruit_Seeds_normalize.html#work_information'>AtGenExpress_PLACE_Fruit_Seeds_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with fruit and seed tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s741i/AtGenExpress_PLACE_Leaf_normalize.html#work_information'>AtGenExpress_PLACE_Leaf_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with leaf tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s741i/AtGenExpress_PLACE_Root_normalize.html#work_information'>AtGenExpress_PLACE_Root_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with root tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s741i/AtGenExpress_PLACE_Seedling_normalize.html#work_information'>AtGenExpress_PLACE_Seedling_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with seedling tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s741i/AtGenExpress_PLACE_Stem_normalize.html#work_information'>AtGenExpress_PLACE_Stem_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with stem tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s741i/AtGenExpress_PLACE_Whole_Plant_normalize.html#work_information'>AtGenExpress_PLACE_Whole_Plant_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with whole plant body parts. </td> </tr> </table>	AtGenExpress_PLACE_Flowering_normalize AtGenExpress_PLACE_Fruit_Seeds_normalize AtGenExpress_PLACE_Leaf_normalize AtGenExpress_PLACE_Root_normalize AtGenExpress_PLACE_Seedling_normalize AtGenExpress_PLACE_Stem_normalize AtGenExpress_PLACE_Whole_Plant_normalize
Rank List of AtGenExpress ATTED mean Contributor:Koro_Nishikata Update:Apr 25, 2013 66 Downloads, 5 Applications Lists for the AtGenExpress and ATTED-II mashup data table. For each experiment, all genes ranked by absolute level of mean expression. <br><br> <strong>References</strong> (for ATTED-II):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17130150">http://www.ncbi.nlm.nih.gov/pubmed/17130150</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s770i/AtGenExpress_ATTED_mean_all.html#work_information'>AtGenExpress_ATTED_mean_all</a> </td> <td> Lists for the AtGenExpress and ATTED-II mashup data table. For each experiment, all genes ranked by absolute level of mean expression. </td> </tr> </table>	AtGenExpress_ATTED_mean_all [motifexpress]
PromoterCAD_links Contributor:GenoCon Update:May 16, 2013 52 Downloads, 16 Applications This will tell the PromoteCAD Application the external link URL of each gene locus.	External_Links [external_links]
Circadian Genomic (DIURNAL + PPDB promoter motif) Contributor:Koro_Nishikata Update:May 10, 2013 834 Downloads, 14 Applications Circadian Data collected over two days (44 hours) at four hour intervals in various growth conditions. We calculated the Phase of each data by non-linear best fit to a sine wave with a 24 hour period, and similarly calculated the Amplitude. Visually checking the 1000 largest amplitude genes showed a good fit in all cases, though a few genes clearly deviated from sinusoidal behavior. All had a major period of 24 hours. For each gene locus, we added the LDSS motifs as calculated by PPDB. Gene Loci without expression data or motif data were removed from this database. <br><br> <strong>References</strong> (for PPDB):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17947329">http://www.ncbi.nlm.nih.gov/pubmed/17947329</a><br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17346352">http://www.ncbi.nlm.nih.gov/pubmed/17346352</a> <br> <strong>References</strong> (for DIURNAL)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18419293">http://www.ncbi.nlm.nih.gov/pubmed/18419293</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_COL_LDHH.html#work_information'>DiurnalHours_PPDB_COL_LDHH</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_COL_SD.html#work_information'>DiurnalHours_PPDB_COL_SD</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_DD_DDHC.html#work_information'>DiurnalHours_PPDB_DD_DDHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Dark (12h) Dark (12h) / Hot (12h) / Cold (12h), and subjected to Dark (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_LDHC.html#work_information'>DiurnalHours_PPDB_LDHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (12h) / Cold (12h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_LDHH_SM.html#work_information'>DiurnalHours_PPDB_LDHH_SM</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h), by using the Smith method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_LDHH_ST.html#work_information'>DiurnalHours_PPDB_LDHH_ST</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h), by using the Stitt method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_LER_SD.html#work_information'>DiurnalHours_PPDB_LER_SD</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler (Landsberg-ereta) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_LIGHT5_HIF138_13.html#work_information'>DiurnalHours_PPDB_LIGHT5_HIF138_13</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis hif138-13 (HETEROGENOUS INBRED FAMILY 138-13) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_LIGHT5_HIF138_8.html#work_information'>DiurnalHours_PPDB_LIGHT5_HIF138_8</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis hif138-8 (HETEROGENOUS INBRED FAMILY 138-8) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_LIGHT5_znknOX.html#work_information'>DiurnalHours_PPDB_LIGHT5_znknOX</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis tsp-ox (hif138-8) (TANDEM ZINCKNUCKLE PROTEIN-ox) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_LL12_LDHH.html#work_information'>DiurnalHours_PPDB_LL12_LDHH</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (24h), and subjected to Light (24h) by the Kay method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_LL23_LDHH.html#work_information'>DiurnalHours_PPDB_LL23_LDHH</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (24h), and subjected to Light (24h) by the Miller method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_LLHC.html#work_information'>DiurnalHours_PPDB_LLHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (12h) / Cold (12h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_LL_LDHC.html#work_information'>DiurnalHours_PPDB_LL_LDHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (12h) / Cold (12h), and subjected to Light (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_LL_LLHC.html#work_information'>DiurnalHours_PPDB_LL_LLHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (12h) / Cold (12h), and subjected to Light (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_lhyox_SD.html#work_information'>DiurnalHours_PPDB_lhyox_SD</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis lhy (lhy-ox) (LATE ELONGATED HYPOCOTYL) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_longday.html#work_information'>DiurnalHours_PPDB_longday</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler strain, grown under the circadian condition of long day light, that is, Light (16h) Dark (8h) by using the Kay method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_lux_2_LDHH.html#work_information'>DiurnalHours_PPDB_lux_2_LDHH</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis lux-2 (LUX ARRHYTHMO-2) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_phyB9_SD.html#work_information'>DiurnalHours_PPDB_phyB9_SD</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis phyB9 (PHYTOCHROME B-9) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s706i/DiurnalHours_PPDB_shortday.html#work_information'>DiurnalHours_PPDB_shortday</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h) by using the Kay method. </td> </tr> </table> <br> <br> <b> <a name="license" style="color:#666666"> License </a> </b> <br> <p> We would like to thank Dr. Yoshiharu Yamamoto for supplying the data of PPDB (Plant Promoter Database) for <a href="http://promotercad.org">PromoterCAD</a> & <a href="http://genocon.org">GenoCon2</a> competition. License of this work's data is according to the intentions of the PPDB original data source.</a> <br> <a href="http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi">http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi</a> </p>	DiurnalHours_PPDB_COL_LDHH DiurnalHours_PPDB_COL_SD DiurnalHours_PPDB_DD_DDHC DiurnalHours_PPDB_LDHC DiurnalHours_PPDB_LDHH_SM DiurnalHours_PPDB_LDHH_ST DiurnalHours_PPDB_LER_SD DiurnalHours_PPDB_LIGHT5_HIF138_13 DiurnalHours_PPDB_LIGHT5_HIF138_8 DiurnalHours_PPDB_LIGHT5_znknOX DiurnalHours_PPDB_LL12_LDHH DiurnalHours_PPDB_LL23_LDHH DiurnalHours_PPDB_LLHC DiurnalHours_PPDB_LL_LDHC DiurnalHours_PPDB_LL_LLHC DiurnalHours_PPDB_lhyox_SD DiurnalHours_PPDB_longday DiurnalHours_PPDB_lux_2_LDHH DiurnalHours_PPDB_phyB9_SD DiurnalHours_PPDB_shortday
Rank Lists of Diurnal PPDB normalize Contributor:Koro_Nishikata Update:May 10, 2013 79 Downloads, 10 Applications Lists for the normalized expression of Diurnal and PPDB mashup data table. For each experiment, all genes ranked by normalized circadian amplitude. <br><br> <strong>References</strong> (for PPDB):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17947329">http://www.ncbi.nlm.nih.gov/pubmed/17947329</a><br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17346352">http://www.ncbi.nlm.nih.gov/pubmed/17346352</a><br> <strong>References</strong> (for Diurnal)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18419293">http://www.ncbi.nlm.nih.gov/pubmed/18419293</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s718i/DiurnalHours_PPDB_normalize_all.html#work_information'>DiurnalHours PPDB normalize all</a> </td> <td> Lists for the DIURNAL and PPDB mashup data table. For each experiment, the all genes ranked by normalized expression level. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s718i/DiurnalHours_PPDB_normalize_GeneRank_for_MotifCircadian_all.html#work_information'>DiurnalHours PPDB normalize GeneRank for MotifCircadian all</a> </td> <td> Lists for the DIURNAL and PPDB (Plant Promoter Database) mashup data table. For each experiment, the all genes ranked by circadian amplitude. </td> </tr> </table> <br> <br> <b> <a name="license" style="color:#666666"> License </a> </b> <br> <p> We would like to thank Dr. Yoshiharu Yamamoto for supplying the data of PPDB (Plant Promoter Database) for <a href="http://promotercad.org">PromoterCAD</a> & <a href="http://genocon.org">GenoCon2</a> competition. License of this work's data is according to the intentions of the PPDB original data source.</a> <br> <a href="http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi">http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi</a> </p>	DiurnalHours_PPDB_normalize_GeneRank_for_MotifCircadian_all [motifcircadian] DiurnalHours_PPDB_normalize_all [motifexpress]
Arabidopsis promoter sequence Contributor:Koro_Nishikata Update:Sep 3, 2013 43 Downloads, 10 Applications <p> Baseline promoter sequences from <i>Arabidopsis</i>, calculated based on the PPDB data and TAIR9 information. </p>	arabidopsis_promoter_sequence [promoter_sequence]
Rank Lists of DIURNAL normalized gene expression + PLACE promoter motif Contributor:Koro_Nishikata Update:Apr 29, 2013 147 Downloads, 6 Applications Lists for the normalized expression of Diurnal and PLACE mashup data table. For each experiment, all genes ranked by normalized circadian amplitude. <br><br> <strong>References</strong> (for PLACE):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/9847208">http://www.ncbi.nlm.nih.gov/pubmed/9847208</a><br> <strong>References</strong> (for DIURNAL)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18419293">http://www.ncbi.nlm.nih.gov/pubmed/18419293</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s751i/DiurnalHours_PLACE_normalize_all_1st.html#work_information'>DiurnalHours PLACE normalize all_1st</a> </td> <td> The 1st half of Lists for the DIURNAL and PLACE mashup data table. For each experiment, the all genes ranked by normalized expression level. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s751i/DiurnalHours_PLACE_normalize_all_2nd.html#work_information'>DiurnalHours PLACE normalize all_2nd</a> </td> <td> The 2nd half of Lists for the DIURNAL and PLACE mashup data table. For each experiment, the all genes ranked by normalized expression level. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s751i/DiurnalHours_PLACE_normalize_GeneRank_for_MotifCircadian_all.html#work_information'>DiurnalHours PLACE normalize GeneRank for MotifCircadian all</a> </td> <td> Lists for the DIURNAL and PLACE mashup data table. For each experiment, the all genes ranked by circadian amplitude. </td> </tr> </table>	DiurnalHours_PLACE_normalize_GeneRank_for_MotifCircadian_all [motifcircadian] DiurnalHours_PLACE_normalize_all_1st [motifexpress] DiurnalHours_PLACE_normalize_all_2nd [motifexpress]
Rank Lists of AtGenExpress median gene expression + PLACE promoter motif Contributor:Koro_Nishikata Update:Apr 29, 2013 50 Downloads, 8 Applications Lists for the AtGenExpress and PLACE mashup data table. For each experiment, all genes ranked by absolute level of median expression. <br><br> <strong>References</strong> (for PLACE)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/9847208">http://www.ncbi.nlm.nih.gov/pubmed/9847208</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s748i/AtGenExpress_PLACE_all.html#work_information'>AtGenExpress_PLACE_all</a> </td> <td> Lists for the AtGenExpress and PLACE mashup data table. For each experiment, the all genes ranked by expression level. </td> </tr> </table>	AtGenExpress_PLACE_all [motifexpress]
Circadian Coexpression (DIURNAL + ATTED-II promoter motif) Contributor:Koro_Nishikata Update:Mar 7, 2013 1243 Downloads, 14 Applications Circadian Data collected over two days (44 hours) at four hour intervals in various growth conditions. We calculated the Phase of each data by non-linear best fit to a sine wave with a 24 hour period, and similarly calculated the Amplitude. Visually checking the 1000 largest amplitude genes showed a good fit in all cases, though a few genes clearly deviated from sinusoidal behavior. All had a major period of 24 hours. For each gene locus, we added the CEG motifs as calculated by ATTED-II. Gene Loci without expression data or motif data were removed from this database. <br><br> <strong>References</strong> (for ATTED-II):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17130150">http://www.ncbi.nlm.nih.gov/pubmed/17130150</a><br> <strong>References</strong> (for DIURNAL)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18419293">http://www.ncbi.nlm.nih.gov/pubmed/18419293</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_COL_LDHH.html#work_information'>DiurnalHours_ATTED_COL_LDHH</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_COL_SD.html#work_information'>DiurnalHours_ATTED_COL_SD</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_DD_DDHC.html#work_information'>DiurnalHours_ATTED_DD_DDHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Dark (12h) Dark (12h) / Hot (12h) / Cold (12h), and subjected to Dark (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_LDHC.html#work_information'>DiurnalHours_ATTED_LDHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (12h) / Cold (12h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_LDHH_SM.html#work_information'>DiurnalHours_ATTED_LDHH_SM</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h), by using the Smith method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_LDHH_ST.html#work_information'>DiurnalHours_ATTED_LDHH_ST</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h), by using the Stitt method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_LER_SD.html#work_information'>DiurnalHours_ATTED_LER_SD</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler (Landsberg-ereta) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_LIGHT5_HIF138_13.html#work_information'>DiurnalHours_ATTED_LIGHT5_HIF138_13</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis hif138-13 (HETEROGENOUS INBRED FAMILY 138-13) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_LIGHT5_HIF138_8.html#work_information'>DiurnalHours_ATTED_LIGHT5_HIF138_8</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis hif138-8 (HETEROGENOUS INBRED FAMILY 138-8) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_LIGHT5_znknOX.html#work_information'>DiurnalHours_ATTED_LIGHT5_znknOX</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis tsp-ox (hif138-8) (TANDEM ZINCKNUCKLE PROTEIN-ox) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_LL12_LDHH.html#work_information'>DiurnalHours_ATTED_LL12_LDHH</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (24h), and subjected to Light (24h) by the Kay method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_LL23_LDHH.html#work_information'>DiurnalHours_ATTED_LL23_LDHH</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (24h), and subjected to Light (24h) by the Miller method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_LLHC.html#work_information'>DiurnalHours_ATTED_LLHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (12h) / Cold (12h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_LL_LDHC.html#work_information'>DiurnalHours_ATTED_LL_LDHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (12h) / Cold (12h), and subjected to Light (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_LL_LLHC.html#work_information'>DiurnalHours_ATTED_LL_LLHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (12h) / Cold (12h), and subjected to Light (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_lhyox_SD.html#work_information'>DiurnalHours_ATTED_lhyox_SD</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis lhy (lhy-ox) (LATE ELONGATED HYPOCOTYL) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_longday.html#work_information'>DiurnalHours_ATTED_longday</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler strain, grown under the circadian condition of long day light, that is, Light (16h) Dark (8h) by using the Kay method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_lux_2_LDHH.html#work_information'>DiurnalHours_ATTED_lux_2_LDHH</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis lux-2 (LUX ARRHYTHMO-2) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_phyB9_SD.html#work_information'>DiurnalHours_ATTED_phyB9_SD</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis phyB9 (PHYTOCHROME B-9) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s586i/DiurnalHours_ATTED_shortday.html#work_information'>DiurnalHours_ATTED_shortday</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h) by using the Kay method. </td> </tr> </table>	DiurnalHours_ATTED_COL_LDHH DiurnalHours_ATTED_COL_SD DiurnalHours_ATTED_DD_DDHC DiurnalHours_ATTED_LDHC DiurnalHours_ATTED_LDHH_SM DiurnalHours_ATTED_LDHH_ST DiurnalHours_ATTED_LER_SD DiurnalHours_ATTED_LIGHT5_HIF138_13 DiurnalHours_ATTED_LIGHT5_HIF138_8 DiurnalHours_ATTED_LIGHT5_znknOX DiurnalHours_ATTED_LL12_LDHH DiurnalHours_ATTED_LL23_LDHH DiurnalHours_ATTED_LLHC DiurnalHours_ATTED_LL_LDHC DiurnalHours_ATTED_LL_LLHC DiurnalHours_ATTED_lhyox_SD DiurnalHours_ATTED_longday DiurnalHours_ATTED_lux_2_LDHH DiurnalHours_ATTED_phyB9_SD DiurnalHours_ATTED_shortday
DIURNAL gene expression + PLACE promoter motif Contributor:Koro_Nishikata Update:Apr 25, 2013 909 Downloads, 6 Applications Circadian Data collected over two days (44 hours) at four hour intervals in various growth conditions. We calculated the Phase of each data by non-linear best fit to a sine wave with a 24 hour period, and similarly calculated the Amplitude. Visually checking the 1000 largest amplitude genes showed a good fit in all cases, though a few genes clearly deviated from sinusoidal behavior. All had a major period of 24 hours. For each gene locus, we added the various sizes of motifs predicted by PLACE (Plant Cis-acting Regulatory DNA Elements) database. Gene Loci without expression data or motif data were removed from this database. <br><br> <strong>References</strong> (for PLACE):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/9847208">http://www.ncbi.nlm.nih.gov/pubmed/9847208</a><br> <strong>References</strong> (for DIURNAL)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18419293">http://www.ncbi.nlm.nih.gov/pubmed/18419293</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_COL_LDHH.html#work_information'>DiurnalHours_PLACE_COL_LDHH</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_COL_SD.html#work_information'>DiurnalHours_PLACE_COL_SD</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_DD_DDHC.html#work_information'>DiurnalHours_PLACE_DD_DDHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Dark (12h) Dark (12h) / Hot (12h) / Cold (12h), and subjected to Dark (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_LDHC.html#work_information'>DiurnalHours_PLACE_LDHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (12h) / Cold (12h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_LDHH_SM.html#work_information'>DiurnalHours_PLACE_LDHH_SM</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h), by using the Smith method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_LDHH_ST.html#work_information'>DiurnalHours_PLACE_LDHH_ST</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h), by using the Stitt method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_LER_SD.html#work_information'>DiurnalHours_PLACE_LER_SD</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler (Landsberg-ereta) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_LIGHT5_HIF138_13.html#work_information'>DiurnalHours_PLACE_LIGHT5_HIF138_13</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis hif138-13 (HETEROGENOUS INBRED FAMILY 138-13) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_LIGHT5_HIF138_8.html#work_information'>DiurnalHours_PLACE_LIGHT5_HIF138_8</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis hif138-8 (HETEROGENOUS INBRED FAMILY 138-8) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_LIGHT5_znknOX.html#work_information'>DiurnalHours_PLACE_LIGHT5_znknOX</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis tsp-ox (hif138-8) (TANDEM ZINCKNUCKLE PROTEIN-ox) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_LL12_LDHH.html#work_information'>DiurnalHours_PLACE_LL12_LDHH</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (24h), and subjected to Light (24h) by the Kay method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_LL23_LDHH.html#work_information'>DiurnalHours_PLACE_LL23_LDHH</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (24h), and subjected to Light (24h) by the Miller method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_LLHC.html#work_information'>DiurnalHours_PLACE_LLHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (12h) / Cold (12h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_LL_LDHC.html#work_information'>DiurnalHours_PLACE_LL_LDHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (12h) / Cold (12h), and subjected to Light (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_LL_LLHC.html#work_information'>DiurnalHours_PLACE_LL_LLHC</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (12h) / Cold (12h), and subjected to Light (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_lhyox_SD.html#work_information'>DiurnalHours_PLACE_lhyox_SD</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis lhy (lhy-ox) (LATE ELONGATED HYPOCOTYL) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_longday.html#work_information'>DiurnalHours_PLACE_longday</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler strain, grown under the circadian condition of long day light, that is, Light (16h) Dark (8h) by using the Kay method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_lux_2_LDHH.html#work_information'>DiurnalHours_PLACE_lux_2_LDHH</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis lux-2 (LUX ARRHYTHMO-2) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_phyB9_SD.html#work_information'>DiurnalHours_PLACE_phyB9_SD</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis phyB9 (PHYTOCHROME B-9) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s746i/DiurnalHours_PLACE_shortday.html#work_information'>DiurnalHours_PLACE_shortday</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h) by using the Kay method. </td> </tr> </table>	DiurnalHours_PLACE_COL_LDHH DiurnalHours_PLACE_COL_SD DiurnalHours_PLACE_DD_DDHC DiurnalHours_PLACE_LDHC DiurnalHours_PLACE_LDHH_SM DiurnalHours_PLACE_LDHH_ST DiurnalHours_PLACE_LER_SD DiurnalHours_PLACE_LIGHT5_HIF138_13 DiurnalHours_PLACE_LIGHT5_HIF138_8 DiurnalHours_PLACE_LIGHT5_znknOX DiurnalHours_PLACE_LL12_LDHH DiurnalHours_PLACE_LL23_LDHH DiurnalHours_PLACE_LLHC DiurnalHours_PLACE_LL_LDHC DiurnalHours_PLACE_LL_LLHC DiurnalHours_PLACE_lhyox_SD DiurnalHours_PLACE_longday DiurnalHours_PLACE_lux_2_LDHH DiurnalHours_PLACE_phyB9_SD DiurnalHours_PLACE_shortday
Rank Lists of AtGenExpress ATTED normalize Contributor:Koro_Nishikata Update:Mar 6, 2013 37 Downloads, 10 Applications Lists for the normalized expression of AtGenExpress and ATTED-II mashup data table. For each experiment, all genes ranked by normalized expression level. <br><br> <strong>References</strong> (for ATTED-II):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17130150">http://www.ncbi.nlm.nih.gov/pubmed/17130150</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s715i/AtGenExpress_ATTED_normalize_all.html#work_information'>AtGenExpress_ATTED_normalize_all</a> </td> <td> Lists for the AtGenExpress and ATTED-II mashup data table. For each experiment, the all genes ranked by normalized expression level. </td> </tr> </table>	AtGenExpress_ATTED_normalize_all [motifexpress]
Rank Lists of AtGenExpress normalized gene expression + PLACE promoter motif Contributor:Koro_Nishikata Update:Apr 29, 2013 46 Downloads, 6 Applications Lists for the normalized expression of AtGenExpress and PLACE mashup data table. For each experiment, all genes ranked by normalized expression level. <br><br> <strong>References</strong> (for PLACE)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/9847208">http://www.ncbi.nlm.nih.gov/pubmed/9847208</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s750i/AtGenExpress_PLACE_normalize_all.html#work_information'>AtGenExpress_PLACE_normalize_all</a> </td> <td> Lists for the AtGenExpress and PLACE mashup data table. For each experiment, the all genes ranked by normalized expression level. </td> </tr> </table>	AtGenExpress_PLACE_normalize_all [motifexpress]
Rank Lists of AtGenExpress PPDB normalize Contributor:Koro_Nishikata Update:Apr 25, 2013 46 Downloads, 10 Applications Lists for the normalized expression of AtGenExpress and PPDB mashup data table. For each experiment, all genes ranked by normalized expression level. <br><br> <strong>References</strong> (for PPDB):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17947329">http://www.ncbi.nlm.nih.gov/pubmed/17947329</a><br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17346352">http://www.ncbi.nlm.nih.gov/pubmed/17346352</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s717i/AtGenExpress_PPDB_normalize_all.html#work_information'>AtGenExpress_PPDB_normalize_all</a> </td> <td> Lists for the AtGenExpress and PPDB (Plant Promoter Database) mashup data table. For each experiment, the all genes ranked by normalized expression level. </td> </tr> </table>	AtGenExpress_PPDB_normalize_all [motifexpress]
Circadian Coexpression (DIURNAL + ATTED-II promoter motif) normalized Contributor:Koro_Nishikata Update:Mar 7, 2013 792 Downloads, 10 Applications Normalized Expression Data of DIURNAL circadian conditions, combined with CEG coexpression analysis regulatory (7mer) motif calculations (ATTED-II). <br><br> <strong>References</strong> (for ATTED-II):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17130150">http://www.ncbi.nlm.nih.gov/pubmed/17130150</a><br> <strong>References</strong> (for DIURNAL)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18419293">http://www.ncbi.nlm.nih.gov/pubmed/18419293</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_COL_LDHH_normalize.html#work_information'>DiurnalHours_ATTED_COL_LDHH_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_COL_SD_normalize.html#work_information'>DiurnalHours_ATTED_COL_SD_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_DD_DDHC_normalize.html#work_information'>DiurnalHours_ATTED_DD_DDHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Dark (12h) Dark (12h) / Hot (12h) / Cold (12h), and subjected to Dark (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_LDHC_normalize.html#work_information'>DiurnalHours_ATTED_LDHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (12h) / Cold (12h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_LDHH_SM_normalize.html#work_information'>DiurnalHours_ATTED_LDHH_SM_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h), by using the Smith method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_LDHH_ST_normalize.html#work_information'>DiurnalHours_ATTED_LDHH_ST_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h), by using the Stitt method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_LER_SD_normalize.html#work_information'>DiurnalHours_ATTED_LER_SD_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler (Landsberg-ereta) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_LIGHT5_HIF138_13_normalize.html#work_information'>DiurnalHours_ATTED_LIGHT5_HIF138_13_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis hif138-13 (HETEROGENOUS INBRED FAMILY 138-13) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_LIGHT5_HIF138_8_normalize.html#work_information'>DiurnalHours_ATTED_LIGHT5_HIF138_8_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis hif138-8 (HETEROGENOUS INBRED FAMILY 138-8) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_LIGHT5_znknOX_normalize.html#work_information'>DiurnalHours_ATTED_LIGHT5_znknOX_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis tsp-ox (hif138-8) (TANDEM ZINCKNUCKLE PROTEIN-ox) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_LL12_LDHH_normalize.html#work_information'>DiurnalHours_ATTED_LL12_LDHH_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (24h), and subjected to Light (24h) by the Kay method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_LL23_LDHH_normalize.html#work_information'>DiurnalHours_ATTED_LL23_LDHH_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (24h), and subjected to Light (24h) by the Miller method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_LLHC_normalize.html#work_information'>DiurnalHours_ATTED_LLHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (12h) / Cold (12h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_LL_LDHC_normalize.html#work_information'>DiurnalHours_ATTED_LL_LDHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (12h) / Cold (12h), and subjected to Light (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_LL_LLHC_normalize.html#work_information'>DiurnalHours_ATTED_LL_LLHC_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (12h) / Cold (12h), and subjected to Light (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_lhyox_SD_normalize.html#work_information'>DiurnalHours_ATTED_lhyox_SD_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis lhy (lhy-ox) (LATE ELONGATED HYPOCOTYL) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_longday_normalize.html#work_information'>DiurnalHours_ATTED_longday_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler strain, grown under the circadian condition of long day light, that is, Light (16h) Dark (8h) by using the Kay method. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_lux_2_LDHH_normalize.html#work_information'>DiurnalHours_ATTED_lux_2_LDHH_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis lux-2 (LUX ARRHYTHMO-2) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_phyB9_SD_normalize.html#work_information'>DiurnalHours_ATTED_phyB9_SD_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis phyB9 (PHYTOCHROME B-9) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s587i/DiurnalHours_ATTED_shortday_normalize.html#work_information'>DiurnalHours_ATTED_shortday_normalize</a> </td> <td> <br> This collection of Gene Expression Properties are associated with the Arabidopsis Ler strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h) by using the Kay method. </td> </tr> </table>	DiurnalHours_ATTED_COL_LDHH_normalize DiurnalHours_ATTED_COL_SD_normalize DiurnalHours_ATTED_DD_DDHC_normalize DiurnalHours_ATTED_LDHC_normalize DiurnalHours_ATTED_LDHH_SM_normalize DiurnalHours_ATTED_LDHH_ST_normalize DiurnalHours_ATTED_LER_SD_normalize DiurnalHours_ATTED_LIGHT5_HIF138_13_normalize DiurnalHours_ATTED_LIGHT5_HIF138_8_normalize DiurnalHours_ATTED_LIGHT5_znknOX_normalize DiurnalHours_ATTED_LL12_LDHH_normalize DiurnalHours_ATTED_LL23_LDHH_normalize DiurnalHours_ATTED_LLHC_normalize DiurnalHours_ATTED_LL_LDHC_normalize DiurnalHours_ATTED_LL_LLHC_normalize DiurnalHours_ATTED_lhyox_SD_normalize DiurnalHours_ATTED_longday_normalize DiurnalHours_ATTED_lux_2_LDHH_normalize DiurnalHours_ATTED_phyB9_SD_normalize DiurnalHours_ATTED_recalculation_COL_SD_normalize DiurnalHours_ATTED_shortday_normalize
Rank Lists of AtGenExpress PPDB Contributor:Koro_Nishikata Update:May 10, 2013 40 Downloads, 16 Applications Lists for the expression of AtGenExpress and PPDB mashup data table. For each experiment, all genes ranked by expression level. <br><br> <strong>References</strong> (for PPDB):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17947329">http://www.ncbi.nlm.nih.gov/pubmed/17947329</a><br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17346352">http://www.ncbi.nlm.nih.gov/pubmed/17346352</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s712i/AtGenExpress_PPDB_all.html#work_information'>AtGenExpress_PPDB_all</a> </td> <td> Lists for the AtGenExpress and PPDB (Plant Promoter Database) mashup data table. For each experiment, the all genes ranked by expression level. </td> </tr> </table> <br> <br> <b> <a name="license" style="color:#666666"> License </a> </b> <br> <p> We would like to thank Dr. Yoshiharu Yamamoto for supplying the data of PPDB (Plant Promoter Database) for <a href="http://promotercad.org">PromoterCAD</a> & <a href="http://genocon.org">GenoCon2</a> competition. License of this work's data is according to the intentions of the PPDB original data source.</a> <br> <a href="http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi">http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi</a> </p>	AtGenExpress_PPDB_all [motifexpress]
PromoterCAD_tooltips Contributor:Koro_Nishikata Update:May 16, 2013 307 Downloads, 13 Applications To facilitate the usability of PromoterCAD, we provide the tooltip informartion. Then it is easy for users to undergo the promoter motif manipulation.	tooltip_AtGenExpress [tooltip] tooltip_DataTable [tooltip] tooltip_PromoterCAD_menus_buttons [tooltip]
Rank Lists of Diurnal ATTED Contributor:Koro_Nishikata Update:Mar 7, 2013 104 Downloads, 14 Applications Lists for the expression of Diurnal and ATTED-II mashup data table. For each experiment, all genes ranked by circadian amplitude. <br><br> <strong>References</strong> (for ATTED-II):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17130150">http://www.ncbi.nlm.nih.gov/pubmed/17130150</a><br> <strong>References</strong> (for Diurnal)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18419293">http://www.ncbi.nlm.nih.gov/pubmed/18419293</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s710i/DiurnalHours_ATTED_all.html#work_information'>DiurnalHours ATTED all</a> </td> <td> Lists for the DIURNAL and ATTED-II mashup data table. For each experiment, the all genes ranked by expression level. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s710i/DiurnalHours_ATTED_GeneRank_for_MotifCircadian_all.html#work_information'>DiurnalHours ATTED GeneRank for MotifCircadian all</a> </td> <td> Lists for the DIURNAL and ATTED-II (Plant Promoter Database) mashup data table. For each experiment, the all genes ranked by circadian amplitude. </td> </tr> </table>	DiurnalHours_ATTED_GeneRank_for_MotifCircadian_all [motifcircadian] DiurnalHours_ATTED_all [motifexpress]
Developmental Coexpression (AtGenExpress gene expression + ATTED-II promoter motif) median Contributor:Koro_Nishikata Update:May 1, 2013 539 Downloads, 16 Applications Developmental Microarray Expression Data (AtGenExpress) of plant developmental tissues, combined with CEG coexpression analysis regulatory (7mer) motif calculations (ATTED-II). We took the median of triplicate measurements from AtGenExpress, then sorted the developmental series into plant organs (Flower, Leaf, Root, Stem, Fruit & Seeds), with one category for seedlings (8 days old or less) and another for whole plants (older than 8 days). Gene Loci without expression data or motif data were removed from this database. <br><br> <strong>References</strong> (for ATTED-II):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17130150">http://www.ncbi.nlm.nih.gov/pubmed/17130150</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s584i/AtGenExpress_ATTED_Flowering_median.html#work_information'>AtGenExpress_ATTED_Flowering_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with flowering tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s584i/AtGenExpress_ATTED_Fruit_Seeds_median.html#work_information'>AtGenExpress_ATTED_Fruit_Seeds_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with fruit and seed tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s584i/AtGenExpress_ATTED_Leaf_median.html#work_information'>AtGenExpress_ATTED_Leaf_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with leaf tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s584i/AtGenExpress_ATTED_Root_median.html#work_information'>AtGenExpress_ATTED_Root_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with root tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s584i/AtGenExpress_ATTED_Seedling_median.html#work_information'>AtGenExpress_ATTED_Seedling_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with seedling tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s584i/AtGenExpress_ATTED_Stem_median.html#work_information'>AtGenExpress_ATTED_Stem_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with stem tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s584i/AtGenExpress_ATTED_Whole_Plant_median.html#work_information'>AtGenExpress_ATTED_Whole_Plant_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with whole plant body parts. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s584i/Heptamer_elements.html#work_information'>Heptamer_elements</a> </td> <td>A list of the 7mer sequence motifs from ATTED-II. This table lists each 7mer along with the calculated CEG value and the position from the TSS of the maximum CEG value.</td> </tr> </table> . </td> </tr> </table>	AtGenExpress_ATTED_Flowering_median AtGenExpress_ATTED_Fruit_Seeds_median AtGenExpress_ATTED_Leaf_median AtGenExpress_ATTED_Root_median AtGenExpress_ATTED_Seedling_median AtGenExpress_ATTED_Stem_median AtGenExpress_ATTED_Whole_Plant_median Heptamer_elements [heptamer]
AtGenExpress mean gene expression + PLACE promoter motif Contributor:Koro_Nishikata Update:Apr 29, 2013 326 Downloads, 5 Applications Developmental Microarray Expression Data (AtGenExpress) of plant developmental tissues, combined with PLACE (Plant Cis-acting Regulatory DNA Elements) motif database. We took the mean of triplicate measurements from AtGenExpress, then sorted the developmental series into plant organs (Flower, Leaf, Root, Stem, Fruit & Seeds), with one category for seedlings (8 days old or less) and another for whole plants (older than 8 days). For each motif, we calculated the position relative to the TSS as determined experimentally. Gene Loci without expression data or motif data were removed from this database. <br><br> <strong>References</strong> (for PLACE)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/9847208">http://www.ncbi.nlm.nih.gov/pubmed/9847208</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s774i/AtGenExpress_PLACE_Flowering_mean.html#work_information'>AtGenExpress_PLACE_Flowering_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with flowering tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s774i/AtGenExpress_PLACE_Fruit_Seeds_mean.html#work_information'>AtGenExpress_PLACE_Fruit_Seeds_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with fruit and seed tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s774i/AtGenExpress_PLACE_Leaf_mean.html#work_information'>AtGenExpress_PLACE_Leaf_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with leaf tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s774i/AtGenExpress_PLACE_Root_mean.html#work_information'>AtGenExpress_PLACE_Root_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with root tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s774i/AtGenExpress_PLACE_Seedling_mean.html#work_information'>AtGenExpress_PLACE_Seedling_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with seedling tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s774i/AtGenExpress_PLACE_Stem_mean.html#work_information'>AtGenExpress_PLACE_Stem_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with stem tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s774i/AtGenExpress_PLACE_Whole_Plant_mean.html#work_information'>AtGenExpress_PLACE_Whole_Plant_mean</a> </td> <td> <br> This collection of Gene Expression Properties are associated with whole plant body parts. </td> </tr> <!-- <tr> <td> <a href='http://linkdata.org/work/rdf1s774i/Heptamer_elements_mean#work_information'>Heptamer_elements</a> </td> <td>A list of the 7mer sequence motifs from ATTED-II. This table lists each 7mer along with the calculated CEG value and the position from the TSS of the maximum CEG value.</td> </tr> --> </table> </td> </tr> </table>	AtGenExpress_PLACE_Flowering_mean AtGenExpress_PLACE_Fruit_Seeds_mean AtGenExpress_PLACE_Leaf_mean AtGenExpress_PLACE_Root_mean AtGenExpress_PLACE_Seedling_mean AtGenExpress_PLACE_Stem_mean AtGenExpress_PLACE_Whole_Plant_mean
Rank List of AtGenExpress PPDB mean Contributor:Koro_Nishikata Update:May 10, 2013 59 Downloads, 5 Applications Lists for the AtGenExpress and PPDB mashup data table. For each experiment, all genes ranked by absolute level of mean expression. <br><br> <strong>References</strong> (for PPDB):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17947329">http://www.ncbi.nlm.nih.gov/pubmed/17947329</a><br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17346352">http://www.ncbi.nlm.nih.gov/pubmed/17346352</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s779i/AtGenExpress_PPDB_mean_all.html#work_information'>AtGenExpress_PPDB_mean_all</a> </td> <td> Lists for the AtGenExpress and PPDB mashup data table. For each experiment, all genes ranked by absolute level of mean expression. </td> </tr> </table> <br> <br> <b> <a name="license" style="color:#666666"> License </a> </b> <br> <p> We would like to thank Dr. Yoshiharu Yamamoto for supplying the data of PPDB (Plant Promoter Database) for <a href="http://promotercad.org">PromoterCAD</a> & <a href="http://genocon.org">GenoCon2</a> competition. License of this work's data is according to the intentions of the PPDB original data source.</a> <br> <a href="http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi">http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi</a> </p>	AtGenExpress_PPDB_mean_all [motifexpress]
Rank Lists of AtGenExpress ATTED Contributor:Koro_Nishikata Update:Apr 22, 2013 56 Downloads, 16 Applications Lists for the expression of AtGenExpress and ATTED-II mashup data table. For each experiment, all genes ranked by expression level. <br><br> <strong>References</strong> (for ATTED-II):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17130150">http://www.ncbi.nlm.nih.gov/pubmed/17130150</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s709i/AtGenExpress_ATTED_all.html#work_information'>AtGenExpress_ATTED_all</a> </td> <td> Lists for the AtGenExpress and ATTED-II mashup data table. For each experiment, the all genes ranked by expression level. </td> </tr> </table>	AtGenExpress_ATTED_all [motifexpress]
Developmental Coexpression (AtGenExpress Developmental gene expression + ATTED-II promoter motif) Triplicate Data Contributor:Koro_Nishikata Update:May 1, 2013 315 Downloads, 7 Applications Full triplicate expression dataset of AtGenExpress plant developmental tissues, combined with CEG coexpression analysis regulatory (7mer) motif calculations (ATTED-II). MotifExpress tool allows the plloting of all triplicate data points during the design process, so the user has some idea of the experimental variation in the measurements. <br><br> <strong>References</strong> (for ATTED-II):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17130150">http://www.ncbi.nlm.nih.gov/pubmed/17130150</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s781i/AtGenExpress_ATTED_Flowering.html#work_information'>AtGenExpress_ATTED_Flowering</a> </td> <td> <br> This collection of Gene Expression Properties are associated with flowering tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s781i/AtGenExpress_ATTED_Fruit_Seeds.html#work_information'>AtGenExpress_ATTED_Fruit_Seeds</a> </td> <td> <br> This collection of Gene Expression Properties are associated with fruit and seed tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s781i/AtGenExpress_ATTED_Leaf.html#work_information'>AtGenExpress_ATTED_Leaf</a> </td> <td> <br> This collection of Gene Expression Properties are associated with leaf tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s781i/AtGenExpress_ATTED_Root.html#work_information'>AtGenExpress_ATTED_Root</a> </td> <td> <br> This collection of Gene Expression Properties are associated with root tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s781i/AtGenExpress_ATTED_Seedling.html#work_information'>AtGenExpress_ATTED_Seedling</a> </td> <td> <br> This collection of Gene Expression Properties are associated with seedling tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s781i/AtGenExpress_ATTED_Stem.html#work_information'>AtGenExpress_ATTED_Stem</a> </td> <td> <br> This collection of Gene Expression Properties are associated with stem tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s781i/AtGenExpress_ATTED_Whole_Plant.html#work_information'>AtGenExpress_ATTED_Whole_Plant</a> </td> <td> <br> This collection of Gene Expression Properties are associated with whole plant body parts. </td> </tr> </table> </td> </tr> </table>	AtGenExpress_ATTED_Flowering AtGenExpress_ATTED_Fruit_Seeds AtGenExpress_ATTED_Leaf AtGenExpress_ATTED_Root AtGenExpress_ATTED_Seedling AtGenExpress_ATTED_Stem AtGenExpress_ATTED_Whole_Plant
AtGenExpress gene expression + PLACE promoter motif Triplicate Data Contributor:Koro_Nishikata Update:May 1, 2013 387 Downloads, 7 Applications Full triplicate expression dataset of AtGenExpress plant developmental tissues, combined with PLACE (Plant Cis-acting Regulatory DNA Elements) motif database. MotifExpress tool allows the plloting of all triplicate data points during the design process, so the user has some idea of the experimental variation in the measurements. <br><br> <strong>References</strong> (for PLACE)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/9847208">http://www.ncbi.nlm.nih.gov/pubmed/9847208</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s783i/AtGenExpress_PLACE_Flowering.html#work_information'>AtGenExpress_PLACE_Flowering</a> </td> <td> <br> This collection of Gene Expression Properties are associated with flowering tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s783i/AtGenExpress_PLACE_Fruit_Seeds.html#work_information'>AtGenExpress_PLACE_Fruit_Seeds</a> </td> <td> <br> This collection of Gene Expression Properties are associated with fruit and seed tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s783i/AtGenExpress_PLACE_Leaf.html#work_information'>AtGenExpress_PLACE_Leaf</a> </td> <td> <br> This collection of Gene Expression Properties are associated with leaf tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s783i/AtGenExpress_PLACE_Root.html#work_information'>AtGenExpress_PLACE_Root</a> </td> <td> <br> This collection of Gene Expression Properties are associated with root tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s783i/AtGenExpress_PLACE_Seedling.html#work_information'>AtGenExpress_PLACE_Seedling</a> </td> <td> <br> This collection of Gene Expression Properties are associated with seedling tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s783i/AtGenExpress_PLACE_Stem.html#work_information'>AtGenExpress_PLACE_Stem</a> </td> <td> <br> This collection of Gene Expression Properties are associated with stem tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s783i/AtGenExpress_PLACE_Whole_Plant.html#work_information'>AtGenExpress_PLACE_Whole_Plant</a> </td> <td> <br> This collection of Gene Expression Properties are associated with whole plant body parts. </td> </tr> <!-- <tr> <td> <a href='http://linkdata.org/work/rdf1s783i/Heptamer_elements.html#work_information'>Heptamer_elements</a> </td> <td>A list of the 7mer sequence motifs from ATTED-II. This table lists each 7mer along with the calculated CEG value and the position from the TSS of the maximum CEG value.</td> </tr> --> </table> </td> </tr> </table>	AtGenExpress_PLACE_Flowering AtGenExpress_PLACE_Fruit_Seeds AtGenExpress_PLACE_Leaf AtGenExpress_PLACE_Root AtGenExpress_PLACE_Seedling AtGenExpress_PLACE_Stem AtGenExpress_PLACE_Whole_Plant
Developmental Genomic (AtGenExpress + PPDB promoter motif) median Contributor:Koro_Nishikata Update:May 10, 2013 409 Downloads, 16 Applications Developmental Microarray Expression Data (AtGenExpress) of plant developmental tissues, combined with LDSS sequence analysis of regulatory (8mer) motif calculations (PPDB). We took the median of triplicate measurements from AtGenExpress, then sorted the developmental series into plant organs (Flower, Leaf, Root, Stem, Fruit & Seeds), with one category for seedlings (8 days old or less) and another for whole plants (older than 8 days). For each motif, we calculated the position relative to the TSS as determined experimentally (PPDB). Gene Loci without expression data or motif data were removed from this database. <br><br> <strong>References</strong> (for PPDB):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17947329">http://www.ncbi.nlm.nih.gov/pubmed/17947329</a><br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17346352">http://www.ncbi.nlm.nih.gov/pubmed/17346352</a> <br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s705i/AtGenExpress_PPDB_Flowering_median.html#work_information'>AtGenExpress_PPDB_Flowering_median</a> </td> <td> This collection of Gene Expression Properties are associated with flowering tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s705i/AtGenExpress_PPDB_Fruit_Seeds_median.html#work_information'>AtGenExpress_PPDB_Fruit_Seeds_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with fruit and seed tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s705i/AtGenExpress_PPDB_Leaf_median.html#work_information'>AtGenExpress_PPDB_Leaf_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with leaf tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s705i/AtGenExpress_PPDB_Root_median.html#work_information'>AtGenExpress_PPDB_Root_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with root tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s705i/AtGenExpress_PPDB_Seedling_median.html#work_information'>AtGenExpress_PPDB_Seedling_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with seedling tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s705i/AtGenExpress_PPDB_Stem_median.html#work_information'>AtGenExpress_PPDB_Stem_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with stem tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s705i/AtGenExpress_PPDB_Whole_Plant_median.html#work_information'>AtGenExpress_PPDB_Whole_Plant_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with whole plant body parts. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s705i/Octamer_elements.html#work_information'>Octamer_elements</a> </td> <td> A list of the 8mer sequence motifs from PPDB. This table lists each 8mer along with the appropriate median position from the TSS, calculated from all 8mers. </td> </tr> </table> <br> <br> <b> <a name="license" style="color:#666666"> License </a> </b> <br> <p> We would like to thank Dr. Yoshiharu Yamamoto for supplying the data of PPDB (Plant Promoter Database) for <a href="http://promotercad.org">PromoterCAD</a> & <a href="http://genocon.org">GenoCon2</a> competition. License of this work's data is according to the intentions of the PPDB original data source.</a> <br> <a href="http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi">http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi</a> </p>	AtGenExpress_PPDB_Flowering_median AtGenExpress_PPDB_Fruit_Seeds_median AtGenExpress_PPDB_Leaf_median AtGenExpress_PPDB_Root_median AtGenExpress_PPDB_Seedling_median AtGenExpress_PPDB_Stem_median AtGenExpress_PPDB_Whole_Plant_median Octamer_elements [octamer]
Rank Lists of Diurnal ATTED normalize Contributor:Koro_Nishikata Update:Mar 7, 2013 122 Downloads, 10 Applications Lists for the normalized expression of Diurnal and ATTED-II mashup data table. For each experiment, all genes ranked by normalized circadian amplitude. <br><br> <strong>References</strong> (for ATTED-II):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17130150">http://www.ncbi.nlm.nih.gov/pubmed/17130150</a><br> <strong>References</strong> (for Diurnal)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18419293">http://www.ncbi.nlm.nih.gov/pubmed/18419293</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s716i/DiurnalHours_ATTED_normalize_all.html#work_information'>DiurnalHours ATTED normalize all</a> </td> <td> Lists for the DIURNAL and ATTED-II mashup data table. For each experiment, the all genes ranked by normalized expression level. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s716i/DiurnalHours_ATTED_normalize_GeneRank_for_MotifCircadian_all.html#work_information'>DiurnalHours ATTED normalize GeneRank for MotifCircadian all</a> </td> <td> Lists for the DIURNAL and ATTED-II (Plant Promoter Database) mashup data table. For each experiment, the all genes ranked by circadian amplitude. </td> </tr> </table>	DiurnalHours_ATTED_normalize_GeneRank_for_MotifCircadian_all [motifcircadian] DiurnalHours_ATTED_normalize_all [motifexpress]
AtGenExpress median gene expression + PLACE promoter motif Contributor:Koro_Nishikata Update:May 1, 2013 385 Downloads, 8 Applications Developmental Microarray Expression Data (AtGenExpress) of plant developmental tissues, combined with PLACE (Plant Cis-acting Regulatory DNA Elements) motif database. We took the median of triplicate measurements from AtGenExpress, then sorted the developmental series into plant organs (Flower, Leaf, Root, Stem, Fruit & Seeds), with one category for seedlings (8 days old or less) and another for whole plants (older than 8 days). For each motif, we calculated the position relative to the TSS as determined experimentally. Gene Loci without expression data or motif data were removed from this database. <br><br> <strong>References</strong> (for PLACE)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/9847208">http://www.ncbi.nlm.nih.gov/pubmed/9847208</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s740i/AtGenExpress_PLACE_Flowering_median.html#work_information'>AtGenExpress_PLACE_Flowering_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with flowering tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s740i/AtGenExpress_PLACE_Fruit_Seeds_median.html#work_information'>AtGenExpress_PLACE_Fruit_Seeds_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with fruit and seed tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s740i/AtGenExpress_PLACE_Leaf_median.html#work_information'>AtGenExpress_PLACE_Leaf_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with leaf tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s740i/AtGenExpress_PLACE_Root_median.html#work_information'>AtGenExpress_PLACE_Root_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with root tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s740i/AtGenExpress_PLACE_Seedling_median.html#work_information'>AtGenExpress_PLACE_Seedling_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with seedling tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s740i/AtGenExpress_PLACE_Stem_median.html#work_information'>AtGenExpress_PLACE_Stem_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with stem tissues. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s740i/AtGenExpress_PLACE_Whole_Plant_median.html#work_information'>AtGenExpress_PLACE_Whole_Plant_median</a> </td> <td> <br> This collection of Gene Expression Properties are associated with whole plant body parts. </td> </tr> <!-- <tr> <td> <a href='http://linkdata.org/work/rdf1s740i/Heptamer_elements.html#work_information'>Heptamer_elements</a> </td> <td>A list of the 7mer sequence motifs from ATTED-II. This table lists each 7mer along with the calculated CEG value and the position from the TSS of the maximum CEG value.</td> </tr> --> </table> </td> </tr> </table>	AtGenExpress_PLACE_Flowering_median AtGenExpress_PLACE_Fruit_Seeds_median AtGenExpress_PLACE_Leaf_median AtGenExpress_PLACE_Root_median AtGenExpress_PLACE_Seedling_median AtGenExpress_PLACE_Stem_median AtGenExpress_PLACE_Whole_Plant_median
Rank Lists of DIURNAL gene expression + PLACE promoter motif Contributor:Koro_Nishikata Update:Apr 25, 2013 100 Downloads, 6 Applications Lists for the Diurnal and PLACE mashup data table. For each experiment, all genes ranked by circadian amplitude. <br><br> <strong>References</strong> (for PLACE):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/9847208">http://www.ncbi.nlm.nih.gov/pubmed/9847208</a><br> <strong>References</strong> (for DIURNAL)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18419293">http://www.ncbi.nlm.nih.gov/pubmed/18419293</a> <br> <br> <br> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s749i/DiurnalHours_PLACE_all.html#work_information'>DiurnalHours PLACE all</a> </td> <td> Lists for the DIURNAL and PLACE mashup data table. For each experiment, the all genes ranked by expression level. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s749i/DiurnalHours_PLACE_GeneRank_for_MotifCircadian_all.html#work_information'>DiurnalHours PLACE GeneRank for MotifCircadian all</a> </td> <td> Lists for the DIURNAL and PLACE mashup data table. For each experiment, the all genes ranked by circadian amplitude. </td> </tr> </table>	DiurnalHours_PLACE_GeneRank_for_MotifCircadian_all [motifcircadian] DiurnalHours_PLACE_all [motifexpress]

Link http://app.linkdata.org/run/app1s335i?tab=readme

<h3>Tooltip</h3>

<p>
To facilitate the usability of PromoterCAD, we provide the tooltip informartion.
Then it is easy for users to undergo the promoter motif manipulation.
<br>
<br>
Hover the cursor to the items such as the button "Start promoter design",
and the PromoterCAD returns the messsage<br>
"Start your promoter design with the empty sequence in the region -51 to -550 from the transcriptional start site."
<br>
<br>
Then users can start their promoter design by clicking the button.
</p>

</td>
<td>

</td>
</tr>
</tbody>
</table>

<h3>Basic Usage</h3>

<p>
To execute the synthetic promoter design using the PromoterCAD, please go through the following workflow basically.
</p>

<table>
<tbody>
<tr valign="top">
<td width="50%">

</td>
<td>

<ol>
<li>
At first, with the menu "Select tool", users can select one of the functions for performing
a particular data operation. For example, the function "MotifMaxExpress" finds
motifs associated with maximum gene expression in a specific condition.
Select this function to find motifs associated with strong expression in flower tissues.
</li>
<li>
With the menu "Analysis Method", users can select a regulatory motif data set (ATTED/PPDB) registered in LinkData.
</li>
<li>
With the menu "Expression Database", users can select microarray expression database (AtGenExpress/DIURNAL) registered in LinkData.
Data containing the developmental series from AtGeneExpress has been split into a series of data tables by tissue type,
and those from DIURNAL has been split into a a series of data tables by circadian growth condition.
</li>
<li>
With the menu "Data Collection", users can select the data tables corresponding to the interesting developmental/circadian condition.
(e.g. "Flowering")
</li>
<li>
The next menu "Select Property", users can select one of the expression conditions
associated with the database. For the AtGenExpress data, this is represented by a
shorthand description. For example, "Col-0_flower" refers to the Columbia strain 0,
grown for 4 weeks until the flowering stage. The gene expression levels are for the
entire flower.
<br>
The full description of each experiment can be referenced on the TAIR website. For
example, flowering experiments are described here:<br>
<a href="http://arabidopsis.org/servlets/TairObject?type=bio_sample_collection&id=1006710
873#437">http://arabidopsis.org/servlets/TairObject?type=bio_sample_collection&id=1006710
873#437</a>
<br>
Select a particular experiment and MotifExpress will find known sequence
motifs associated with high expression in this condition. MotifMaxExpress will
automatically display these motif sequences (in this case septamers) in line with the
base promoter sequence at the same location as they occur in the promoter returned
by MotifExpress.
</li>
<li>
By clicking the button "Add motif", all the selected motifs are incorporated into the promoter motif skelton. The result will be displayed in the text area
 with the motifs indicated by color.
</li>
<li>
Click the button "Next", to repeat the sequence design operation and continue the
workflow. (Continues the steps 1-6.)
</li>
<li>
In the final step, click the button "Finish Now" to  fill in the skeleton (the 'bones' of the promoter, containing just regulatory motifs and the minimal promoter region) with the remaining sequence.
This will replace the blank '-' sequences, but will preserve any motifs added in the design process.
</li>
</ol>

</td>
</tr>
</tbody>
</table>

<h3>Tutorials</h3>

<p>
Here are tutorials to execute synthetic promoter designs using PromoterCAD. These have example walk throughs with snapshots for each step.
</p>
<table>

<tbody>
<tr valign="top">
<td>
<a target="_blank" href="https://hackpad.com/fvol30isGPL#PromoterCAD-Beginning-Tutorial-1">
Beginning_Tutorials_1
</a>
</td>
<td>
This tutorial illustrates how to design a synthetic promoter for Leaf specific expression using the MotifExpress tool.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/oNrS0K21sgd#PromoterCAD-Beginning-Tutorial-2:-Design-a-promoter-for-Circadian-expression-with-MotifCircadian">
Beginning_Tutorials_2
</a>
</td>
<td>
This tutorial illustrates how to design a synthetic promoter for Circadian expression with MotifCircadian tool.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/dAL1Omja3Mi#PromoterCAD-Beginning-Tutorial-3:-Use-InputMotif-to-add-specific-motifs-to-a-gene-design">
Beginning_Tutorials_3
</a>
</td>
<td>
This tutorial illustrates how to use InputMotif tool to add specific motifs to a gene design.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/4b72OO5mXOa#Advanced-Tutorial-1:-How-to-fork-your-own-PromoterCAD-workspace-and-make-workflow-snapshots">
Advanced_Tutorials_1
</a>
</td>
<td>
This tutorial illustrates how to fork your own PromoterCAD workspace.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/sxhIWdJ8Qix#Advanced-Tutorial-2A:-add-a-new-database-(normalized-data)-to-PromoterCAD">
Advanced_Tutorials_2A
</a>
</td>
<td>
This tutorial illustrates how to add a new normalized data to PromoterCAD.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/IWlEhmJ2jfT#Advanced-Tutorial-2B:-add-a-new-database-(PLACE-motif-data)-to-PromoterCAD">
Advanced_Tutorials_2B
</a>
</td>
<td>
This tutorial illustrates how to add a new database PLACE motif data to PromoterCAD.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/SLPqFU0AiLn#Advanced-Tutorial-3A:-Add-a-new-gene-expression-mining-plugin-to-PromoterCAD-(MotifRanking)">
Advanced_Tutorials_3A
</a>
</td>
<td>
This tutorial illustrates how to add a new data mining plugin tool MotifRanking.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/fzxSQrVTkdB#Advanced-Tutorial-3B:-Add-a-new-data-mining-plugin-to-PromoterCAD-(MotifNonCircadian)">
Advanced_Tutorials_3B
</a>
</td>
<td>
This tutorial illustrates how to add a new data mining plugin tool MotifNonCircadian.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/Advanced-Tutorial-4-cJ1VVvUtp1W">
Advanced_Tutorials_4
</a>
</td>
<td>
This tutorial illustrates how to modify and upload your own tooltips.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/Help-Page-Interpreting-PromoterCAD-Output-VnHPootms0p">
Help Page
</a>
</td>
<td>
Interpreting PromoterCAD Output 
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/Help-Page-How-to-tag-input-LinkData-tables-for-PromoterCAD-3WwOXIeohDL">
Help Page
</a>
</td>
<td>
How to tag input LinkData tables for PromoterCAD 
</td>
</tr>

</tbody>
</table>

<h3>License</h3>
<p>
PromoterCAD source code is licensed under  <a href="http://opensource.org/licenses/LGPL-3.0">the LGPL-3.0 license (the GNU Lesser General Public License, version 3.0)</a> and <a href="http://creativecommons.org/licenses/by-sa/3.0/deed.en">the Creative Commons license CC-BY-SA</a>.
So users can fork the source code of PromoterCAD to easily create their own data mining plugins. 
<br>
<a href="http://creativecommons.org/licenses/by-sa/3.0/deed.en">
<img src="http://app.linkdata.org/asset/8c72b4fc.png" width="20%">
</a>

</p>