MotifRanking｜Mash up the Linked Open Data

about this App

MotifRanking

MotifRanking = function( containerId, options ){
	var app = new Application.motifRanking( containerId, options );
};

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

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

Application.motifRanking.prototype = {
	_containerId : null,
	_baseSequence : null,
	_options : null,
	_motifProperty : null,
	_heptamer : null,
	_octamer : null,
	_appSequence : null,
	_filteredSubjectList : null,
	_motifViewDialogId : null,
	_geneInfoContainerId : null,
	
	_default : {
		appName : "MotifRanking",
		selectPropertyCaption : "Select Property",
		selectPropertyAreaClass : "selectPropertyArea",
		selectPropertyClass : "selectProperty",
		
		// 発現ランキング関係の定数
		selectRankingCaption : "Expression Ranking",
		selectRankingAreaClass : "selecRankingArea",
		selectRankingClass : "selectRanking",
		rankingRange : 10,
		
		// 順序選択関係の定数
		selectOrderCaption : "Order",
		selectOrderAreaClass : "selectOrderArea",
		selectOrderName : "selectOrder",
		topValue : "top",
		bottomValue : "bottom",
		topLabel : "Top",
		bottomLabel : "Bottom",
		
		resultAreaClass : "resultArea",
		replaceButtonAreaClass : "replaceButtonArea",
		replaceButtonClass : "replaceButton",
		nextButtonAreaClass : "nextButtonArea",
		replaceSequenceClass : "replaceSequence",
		errorMessageAreaClass : "errorMessage",
		dialogErrorMessageClass : "dialogErrorMessage",
		dialogOutRangeValueMessage : "Please input a value between {0} and {1}",
		databaseInfoClass : "databaseInfo",
		geneLabelClass : "geneUrl",
		geneInfoLinkClass : "geneInfoLink",
		motifSequenceProperty : "motif sequence",
		motifPositionProperty : "motif position",
		typeProperty : "type",
		validType : "REG",
		motifViewDialogId : "motifViewDialog",
		motifViewDialogClass : "motifViewDialog",
		motifViewDialogTitle : "Motif View",
		minSequenceClass : "minSeq",
		maxSequenceClass : "maxSeq",
		websiteNameAtted : "ATTED",
		websiteNamePpdb : "PPDB",
		baseSequenceMinLength : 50,
		dialogImageUrl : "http://app.linkdata.org/asset/a06f4de4.png",
		callback : function() {},
		loadingImageContainer : "loadingImageContainer",
		loadingImageUrl : "http://app.linkdata.org/asset/67556085.gif",
		loadingMessageClass : "loadingMessage",
		loadingMessage : "Loading linked data, it may take a few minutes..."
	},
	
	_tag : {
		topResult : "result_top",
		bottomResult : "result_bottom"
	},
	
	_init : function( containerId, options ) {
		this._containerId = containerId;
		this._options = $.extend( {}, this._default, options );
		this._baseSequence = this._options.baseSequence;
		this.filteredSubjectList = [];
		var date = new Date();
		this._geneInfoContainerId = "gene_info_containerId_" + date.getTime();
		this._initMotifProperty(this._options);
		this._initAppSequence(this._options);
		this._initHeptamer();
		this._initOctamer();
		this._initView();
		this._initMotifViewDialog();
	},
	
	_initMotifProperty : function( opts ) {
		var obj = {
			workId : opts.workId,
			fileName : opts.fileName
		};
		this._motifProperty = new Application.motifProperty( obj );
	},
	
	_initAppSequence : function( opts ) {
		var self = this;
		var timer = new Application.timer();
		var init = function() {
			var seqProperty = self._motifProperty.getPropertyByLabel( self._options.motifSequenceProperty );
			var posProperty = self._motifProperty.getPropertyByLabel( self._options.motifPositionProperty );
			if( seqProperty && posProperty )
			{
				var obj = {
					workId : opts.workId,
					fileName : opts.fileName,
					baseSequence : self._baseSequence,
					motifSequenceProperty : seqProperty,
					motifPositionProperty : posProperty,
					containerId : self._containerId,
					errorMessageClass : self._options.errorMessageAreaClass,
					baseSequenceMinLength : self._options.baseSequenceMinLength
				};
				self._appSequence = new Application.sequence( obj );
			}
			else
			{
				timer.call( init );
			}
		};
		init();
	},
	
	_initHeptamer : function() {
		this._heptamer = new Application.heptamer();
	},
	
	_initOctamer : function() {
		this._octamer = new Application.octamer();
	},
	
	_initView : function() {
		this._initMainView();
		this._initDialogView();
	},
	
	_initMainView : function() {
		var self = this;
		var timer = new Application.timer();
		var fillOptionMethod = function() {
			var optionArray = self._motifProperty.getOptionArray();
			if( optionArray )
			{
				var sb = [];
				sb[ sb.length ] = "<div class='" + self._options.selectPropertyAreaClass + " row'>";
				sb[ sb.length ] = " <div class='label left'>" + self._options.selectPropertyCaption + "</div>";
				sb[ sb.length ] = " <div class='left'>";
				sb[ sb.length ] = "  <select class='" + self._options.selectPropertyClass + "'>";
				sb[ sb.length ] = "   <option value='" + -1 + "'>-- Select Property --</option>";
				$.each( optionArray, function( key, obj ) {
					sb[sb.length] = "<option value='" + obj.key + "'>" + obj.value + "</option>";
				} );
				sb[ sb.length ] = "  </select>";
				sb[ sb.length ] = " </div>";
				sb[ sb.length ] = "</div>";
				
				// 順序の選択のためのエリア
				sb[ sb.length ] = "<div class='" + self._options.selectOrderAreaClass + " row hidden'>";
				sb[ sb.length ] = " <div class='label left'>" + self._options.selectOrderCaption + "</div>";
				sb[ sb.length ] = " <div class='left'>";
				sb[ sb.length ] = "  <lable><input name='" + self._options.selectOrderName + "'";
				sb[ sb.length ] = "   type='radio' value='" + self._options.topValue +"'>" + self._options.topLabel + "</label>";
				sb[ sb.length ] = "  <label><input name='" + self._options.selectOrderName + "'";
				sb[ sb.length ] = "   type='radio' value='"+ self._options.bottomValue +"'>" + self._options.bottomLabel + "</label>";
				sb[ sb.length ] = " </div>";
				sb[ sb.length ] = "</div>";
				
				//発現ランキングのエリア
				sb[ sb.length ] = "<div class='" + self._options.selectRankingAreaClass + " row hidden'>";
				sb[ sb.length ] = " <div class='label left'>" + self._options.selectRankingCaption + "</div>";
				sb[ sb.length ] = " <div class='left'>";
				sb[ sb.length ] = "  <select class='" + self._options.selectRankingClass + "'>";
				sb[ sb.length ] = "   <option value='" + -1 + "'>-- Select Gene --</option>";
				sb[ sb.length ] = "  </select>";
				sb[ sb.length ] = " </div>";
				sb[ sb.length ] = "</div>";
				
				sb[ sb.length ] = "<div class='" + self._options.databaseInfoClass + " hidden'></div>";
				sb[ sb.length ] = "<div id='" + self._geneInfoContainerId + "'></div>";
				sb[ sb.length ] = "<div class='" + self._options.resultAreaClass + " hidden'></div>";
				sb[ sb.length ] = "<div class='" + self._options.errorMessageAreaClass + " hidden'>error</div>";
				sb[ sb.length ] = "<div class='" + self._options.replaceButtonAreaClass + " hidden'>";
				sb[ sb.length ] = "<a class='" + self._options.replaceButtonClass + " btn btn-lightblue'>Replace</a>";
				sb[ sb.length ] = "</div>";
				sb[ sb.length ] = "<div class='" + self._options.replaceSequenceClass + " hidden'></div>";
				sb[ sb.length ] = "<div class='" + self._options.loadingImageContainer + " hidden' align='center'>";
				sb[ sb.length ] = "<div class='" + self._options.loadingMessageClass + "'>" + self._options.loadingMessage + "</div>";
				sb[ sb.length ] = "<div>";
				sb[ sb.length ] = "<img src='" + self._options.loadingImageUrl + "'/>";
				sb[ sb.length ] = "</div>";
				sb[ sb.length ] = "</div>";
				$( "#" + self._containerId ).html( sb.join( "" ) );
				
				// イベントに関数をバインドする処理
				self._initSelectPropertyListener();
				self._initSelectOrderListener();
				self._initRankingListener();
			}
			else
			{
				timer.call(fillOptionMethod);
			}
		};
		fillOptionMethod();
	},
	
	_initDialogView : function() {
		var sb = [], self = this, date = new Date(); 
		this._motifViewDialogId = "motifViewDialog_id_" + self._containerId + "_" + date.getTime();
		sb[ sb.length ] = "<div id='" + this._motifViewDialogId + "' class='hidden'>";
		sb[ sb.length ] = "<input type='hidden' class='sequence'>";
		sb[ sb.length ] = "<div>";
		sb[ sb.length ] = "<span>Place motif at position</span>";
		sb[ sb.length ] = "<input type='text' class='position'/>";
		sb[ sb.length ] = "</div>";
		sb[ sb.length ] = "<div>";
		sb[ sb.length ] = "<span class='explanation'>Replace with prefer position between ";
		sb[ sb.length ] = "<span class='minSeq'></span> and <span class='maxSeq'>";
		sb[ sb.length ] = "</span>";
		sb[ sb.length ] = "</div>";
		sb[ sb.length ] = "<div>";
		sb[ sb.length ] = "<span>Number of extra copies</span>";
		sb[ sb.length ] = "<input type='text' class='extraCopies' value='0'/>";
		sb[ sb.length ] = "</div>";
		sb[ sb.length ] = "<div>";
		sb[ sb.length ] = "<span>Space between copies (Base Pairs)</span>";
		sb[ sb.length ] = "<input type='text' class='basePairs' value='0'/>";
		sb[ sb.length ] = "</div>";
		sb[ sb.length ] = "<div class='motifImageArea'>";
		sb[ sb.length ] = "<img src='" + this._options.dialogImageUrl + "'/>";
		sb[ sb.length ] = "</div>";
		sb[ sb.length ] = "<div>";
		sb[ sb.length ] = "<span class='explanation'>Click ";
		sb[ sb.length ] = "<a class='moreInfo'>here</a> to see the additional information about motif from " + self._getDataBaseWebsiteName() + " website";
		sb[ sb.length ] = "</span>";
		sb[ sb.length ] = "</div>";
		sb[ sb.length ] = "<div>";
		sb[ sb.length ] = "<span class='dialogErrorMessage errorMessage hidden'></span>";
		sb[ sb.length ] = "</div>";
		sb[ sb.length ] = "</div>";
		$( "#" + this._containerId ).append( sb.join( "" ) );
	},
	
	_initSelectPropertyListener : function() {
		var self = this, workId = self._options.workId, fileName = self._options.fileName;
		var timer = new Application.timer();
		var setSelectListener = function() {
			if($( "#" + self._containerId + " ." + self._options.selectPropertyClass ).length !== 0 )
			{
				$( "#" + self._containerId + " ." + self._options.selectPropertyClass ).change( function() {
					// すでに後続の部品がすでに表示されている場合に備え、それらを一旦隠す。
					self._appSequence.hideError();
					$( "#" + self._containerId + " ." + self._options.selectOrderAreaClass ).hide();
					$( "#" + self._containerId + " ." + self._options.selectRankingAreaClass ).hide();
					$( "#" + self._containerId + " ." + self._options.resultAreaClass ).hide();
					$( "#" + self._containerId + " ." + self._options.replaceButtonAreaClass ).hide();
					$( "#" + self._containerId + " ." + self._options.replaceSequenceClass ).hide();
					$( "#" + self._containerId + " ." + self._options.databaseInfoClass ).hide();
					$( "#" + self._containerId + " #" + self._geneInfoContainerId ).hide();
					// 順序選択のためのラジオボタンをリセット
					$( "#" + self._containerId + " [name=" + self._options.selectOrderName + "]" ).attr( "checked", false );
					// 選択されたのが「-- Select Property --」でなければ
					if( $( this ).val() !== "-1" )
					{
						$( "#" + self._containerId + " ." + self._options.selectOrderAreaClass ).show();
					}
				} );
			}
			else
			{
				timer.call( setSelectListener );
			}
		};
		setSelectListener();
	},
	
	_initSelectOrderListener : function() {
		var self = this, workId = self._options.workId, fileName = self._options.fileName;
		var timer = new Application.timer();
		var setSelectListener = function() {
				if( $( "#" + self._containerId + " [name=" + self._options.selectOrderName + "]" ).length !== 0 )
				{
					$( "#" + self._containerId + " [name=" + self._options.selectOrderName + "]" ).change( function() {
						// ロード中の表示
						$( "#" + self._containerId + " ." + self._options.loadingImageContainer ).show();
						// すでに後続の部品がすでに表示されている場合に備え、それらを一旦隠す。
						self._appSequence.hideError();
						$( "#" + self._containerId + " ." + self._options.selectRankingAreaClass ).hide();
						$( "#" + self._containerId + " ." + self._options.resultAreaClass ).hide();
						$( "#" + self._containerId + " ." + self._options.replaceButtonAreaClass ).hide();
						$( "#" + self._containerId + " ." + self._options.replaceSequenceClass ).hide();
						$( "#" + self._containerId + " ." + self._options.databaseInfoClass ).hide();
						$( "#" + self._containerId + " #" + self._geneInfoContainerId ).hide();
						
						var propLabel = $( "#" + self._containerId + " ." + self._options.selectPropertyClass + " option:selected" ).val();
						var order = $( this ).val();
						// ランキング生成へ
						self._showMotifSequence( workId, fileName, propLabel, order );
					} );
				}
				else
				{
					timer.call( setSelectListener );
				}
			};
		setSelectListener();
	},
	
	_initRankingListener : function() {
		var self = this, workId = self._options.workId, fileName = self._options.fileName;
		var timer = new Application.timer();
		var setSelectListener = function() {
			if($( "#" + self._containerId + " ." + self._options.selectRankingClass ).length !== 0 ) {
				$( "#" + self._containerId + " ." + self._options.selectRankingClass ).change( function() {
					// すでに後続の部品がすでに表示されている場合に備え、それらを一旦隠す。
					self._appSequence.hideError();
					$( "#" + self._containerId + " ." + self._options.resultAreaClass ).hide();
					$( "#" + self._containerId + " ." + self._options.replaceButtonAreaClass ).hide();
					$( "#" + self._containerId + " ." + self._options.replaceSequenceClass ).hide();
					$( "#" + self._containerId + " ." + self._options.databaseInfoClass ).hide();
					$( "#" + self._containerId + " #" + self._geneInfoContainerId ).hide();
					// 選択されたのが「-- Select Gene --」でなければ
					if( $( this ).val() !== "-1" )
					{
						$( "#" + self._containerId + " ." + self._options.loadingImageContainer ).show();
						var subject = $( "option:selected", this ).val();
						var propLabel = $( "#" + self._containerId + " ." + self._options.selectPropertyClass + " option:selected" ).val();
						self._motifSequence( workId, fileName, subject, propLabel );
					}
				} );
			}
			else
			{
				timer.call( setSelectListener );
			}
		};
		setSelectListener();
	},
	
	_showGenePlot : function( subject, property ) {
		var self = this;
		$( "#" + self._containerId + " #" + self._geneInfoContainerId ).show();
		var options = {
			workId : self._options.workId,
			fileName : self._options.fileName,
			subject : subject,
			property : property
		};
		var app = new Application.geneChart( self._geneInfoContainerId, options );
	},
	
	_showDataBaseInformationList : function() {
		var self = this, seqVal = [];
		$( "#" + self._containerId + " .userSequence .hdnSequence" ).each( function() {
			var tmpPos = $( this ).siblings( ".hdnPosition" ).val();
			seqVal.push( $( this ).val() + "[" + tmpPos + "]" );
		} );
		self._showDatabaseInfo( seqVal.join( ", " ) );
	},
	
	_initReplaceButtonLitener : function() {
		var self = this, workId = self._options.workId, fileName = self._options.fileName;
		$( "#" + self._containerId + " ." + self._options.replaceButtonClass ).click( function() {
			self._appSequence.hideError();
			$( "#" + self._containerId + " ." + self._options.replaceSequenceClass ).show();
			var seqs = [];
			$( "#" + self._containerId + " .userSequence" ).each( function() {
				seqs.push($( this ).text() );
			} );
			var html = self._appSequence.replace( seqs );
			$( "#" + self._containerId + " ." + self._options.replaceSequenceClass ).html( html );
			self._showDataBaseInformationList();
			self._options.callback();
		} );
	},
	
	_initMotifSequenceListener : function() {
		var self = this;
		$( "#" + self._containerId + " .motifSequence" ).click( function() {
			$( "." + self._options.motifViewDialogClass ).hide();
			var parent = $( this ).closest( ".userSequence" );
			var container = $( this ).closest( ".userSequence" );
			var seq = $( parent ).find( ".hdnSequence" ).val();
			var pos = $( parent ).find( ".hdnPosition" ).val();
			var seqEl = self._getSeqElBySeq( seq );
			var appropriatePos = ( seqEl && seqEl.getAppropriatePos() ) ? seqEl.getAppropriatePos() : pos;
			self._initSequencePopup( seqEl );
			$( "#" + self._motifViewDialogId + " ." + self._options.dialogErrorMessageClass ).hide();
			$( "#" + self._motifViewDialogId + " .sequence" ).val( seq );
			$( "#" + self._motifViewDialogId + " .position" ).val( appropriatePos );
			$( "#" + self._motifViewDialogId + " .extraCopies" ).val( 0 );
			$( "#" + self._motifViewDialogId + " .basePairs" ).val( 0 );
			$( "#" + self._motifViewDialogId + " .minSeq" ).html( self._getMinPosition( seq ) );
			$( "#" + self._motifViewDialogId + " .maxSeq" ).html( self._getMaxPosition( seq ) );
			self._initPositionInsert( seq, appropriatePos );
			$( "#" + self._motifViewDialogId ).dialog( { title: self._default.motifViewDialogTitle + " - " + seq } );
			$( "#" + self._motifViewDialogId ).dialog( "open" );
			$( "#" + self._motifViewDialogId ).closest( '.' + self._options.motifViewDialogClass ).show();
		} );
	},
	
	_initSequencePopup : function( seqEl ) {
		var self = this;
		$( "#" + self._motifViewDialogId + " .moreInfo" ).unbind( "click" );
		var url = ( seqEl && seqEl.getExternalUrl() ) ? seqEl.getExternalUrl() : "#";
		$( "#" + self._motifViewDialogId + " .moreInfo" ).click( function() {
			self._showPopupWindow( url );
		} );
	},
	
	_showPopupWindow : function( url ) {
		var winWidth = 800;
		var winHeight = 800;
		var winLeft = parseInt( ( screen.availWidth / 2 ) - ( winWidth / 2 ), 10 );
		var winTop = parseInt( ( screen.availHeight / 2 ) - ( winHeight / 2 ), 10 );
		var winStyle = "width=" + winWidth + ",height=" + winHeight + ",left=" + winLeft + ",top="
			+ winTop + ",screenX=" + winLeft + ",screenY=" + winTop + ",scrollbars=1";
		window.open( url, "Motif", winStyle );
	},
	
	_initPositionInsert : function( seq, pos ) {
		var self = this;
		var mod = seq.length % 2;
		$( "#" + self._motifViewDialogId + " .position" ).unbind( "keyup" );
		$( "#" + self._motifViewDialogId + " .position" ).keyup( function() {
			var val = $( this ).val();
			if( isNaN( val ) ) {
				$( this ).val( pos );
				return;
			}
			var tmpVal = val.toString();
			if( mod === 0 )
			{
				if( tmpVal.indexOf( "." ) === -1 )
				{
					$( this ).val( tmpVal + ".5" );
				}
				else
				{
					$( this ).val( tmpVal.split( "." )[ 0 ] + ".5" );
				}
			}
			else
			{
				if( tmpVal.indexOf( "." ) > -1 )
				{
					$( this ).val( tmpVal.split( "." )[ 0 ] );
				}
			}
		} );
	},
	
	_initMotifViewDialog : function() {
		var self = this;
		$( "#" + self._motifViewDialogId).dialog( {
			autoOpen: false,
			title: self._default.motifViewDialogTitle,
			width: 520,
			dialogClass : self._options.motifViewDialogClass,
			buttons : [
				{
					text: "Replace",
					click : function() {
						var seq = $( "#" + self._motifViewDialogId ).find( ".sequence" ).val();
						var pos = $( "#" + self._motifViewDialogId ).find( ".position" ).val();
						var extraCopies = parseInt( $( "#" + self._motifViewDialogId ).find( ".extraCopies" ).val(), 10 );
						var basePairs = parseInt( $( "#" + self._motifViewDialogId ).find( ".basePairs" ).val(), 10 );
						var minPos = parseFloat( $( "#" + self._motifViewDialogId ).find( ".minSeq" ).html(), 10 );
						var maxPos = parseFloat( $( "#" + self._motifViewDialogId ).find( ".maxSeq" ).html(), 10 );
						if( minPos > pos || maxPos < pos ) {
							$dialogError = $( "#" + self._motifViewDialogId + " ." + self._options.dialogErrorMessageClass );
							$dialogError.html( self._options.dialogOutRangeValueMessage.replace( "{0}", minPos ).replace( "{1}", maxPos ) );
							$dialogError.show();
							return;
						}
						self._appSequence.hideError();
						self._replaceWithSequence( seq, pos, extraCopies, basePairs );
						$(this).dialog( "close" );
					}
				},
				{
					text: "Cancel",
					click : function() {
						$(this).dialog( "close" );
					}
				}
			]
		} );
	},
	
	//要約ファイル(処理速度向上のために発現量が上位あるいは下位の遺伝子をリストアップしたファイル)がない場合に発現を最大にするモチーフを取り出す
	_getMotifTripleRanking : function( workId, fileName, property, order ) {
		var self = this;
		// まずは8000件を読み込む
		var index = new Application.index(1, 8000);
		var totalList = [];
		var getTriplesByProperty = function( tripleList ) {
			// 新たに読み込んだtripleの配列を連結
			totalList = totalList.concat( tripleList );
			// まだ続きがあれば次の8000件を読み込む
			if( tripleList && tripleList.length === index.getItemCount() ) {
				//再帰的に繰り返し。
				LinkData.getTriplesByProperty( workId, fileName, property, getTriplesByProperty, index.increment() );
			}
			else
			{
				var i;
				var subjects = [];
				var len = totalList.length;
				var cnt = 0;
				// 順序を切り替えるための係数
				var sign = ( order === self._options.topValue ) ? 1 : -1;
				// 発現量でソート
				totalList.sort( function( a, b ) { return (b.object - a.object) * sign; } );
				// 所定の個数のsubjectが集まるか、全subjectを読み切るまでループ
				for( i = 0; i < len && cnt < self._options.rankingRange; i++ )
				{
					// 重複のチェック
					var j;
					for( j = 0; j < cnt; j++ )
					{
						if( totalList[ i ].subject === subjects[ j ] )
						{
							break;
						}
					}
					// 重複がなければランキングに追加
					if( j === cnt )
					{
						subjects[ cnt++ ] = totalList[ i ].subject;
					}
				}
				self._showRanking( subjects );
			}
		};
		
		//データベースからtriplesを読み込み、getTriplesByPropertyにそれを渡す。
		LinkData.getTriplesByProperty( workId, fileName, property, getTriplesByProperty, index.getIndex() );
	},
	
	//発現ランキングの生成
	_showRanking : function( subjects ) {
		var self = this;
		var $select = $( "#" + self._containerId + " ." + self._options.selectRankingClass );
		$( "option", $select ).remove();
		$select.append( "<option value='-1'>-- Select Gene --</option>" );
		$.each( subjects, function( tKey, tValue ) {
			var gene = self._motifProperty.getGeneBySubject( tValue );
			$select.append( "<option value='" + tValue + "'>" + ( tKey + 1 ) + ":" + gene + "</option>" );
		} );
		$( "#" + self._containerId + " ." + self._options.loadingImageContainer ).hide();
		$( "#" + self._containerId + " ." + self._options.selectRankingAreaClass ).show();
	},
	
	// 下記関数内で要約ファイルがある場合とない場合に分岐
	_showMotifSequence : function( workId, fileName, propLabel, order ) {
		var self = this, foundAbstractFile = false;
		var getFilesByTag = function( resultList ) {
			$.each( resultList, function( wId, fileList ) {
				$.each( fileList, function( fileKey, fName ) {
					var tmpName;
					// 要約ファイルの有無の判定の準備
					if( order === self._options.topValue )
					{
						tmpName = fName.split( "_top" );
					}
					else
					{
						tmpName = fName.split( "_bottom" );
					}
					
					if(fileName.indexOf( tmpName[ 0 ] ) > -1 )
					{
						// 要約ファイルが存在する場合
						self._getAbstractFilePropertyList( workId, fileName, wId, fName, propLabel );
						foundAbstractFile = true;
						return false;
					}
				} );
			} );
			if( !foundAbstractFile )
			{
				// 要約ファイルが存在しない場合
				var property = self._motifProperty.getPropertyByLabel( propLabel );
				self._getMotifTripleRanking( workId, fileName, property, order );
			}
		};
		LinkData.getFilesByTag( null, self._tag.topResult, getFilesByTag );
	},
	
	_getAbstractFilePropertyList : function( workId, fileName, topWorkId, topFileName, propLabel ) {
		var self = this;
		var getProperties = function( propList ) {
			$.each(propList, function( propKey, propValue ) {
				var tmpProperty = self._motifProperty._getLabel( propValue );
				if( tmpProperty.indexOf( propLabel ) > -1 )
				{
					var property = self._motifProperty.getPropertyByLabel( propLabel );
					self._showMotif( workId, fileName, property, topWorkId, topFileName, propValue );
					return false;
				}
			} );
		};
		LinkData.getProperties( topWorkId, topFileName, getProperties );
	},
	
	_showMotif : function( workId, fileName, property, topWorkId, topFileName, topProperty ) {
		var self = this;
		var index = new Application.index( 1, 1000 );
		var getTriplesByProperty = function( tripleList ) {
			self._showMotifByTripleList( workId, fileName, property, tripleList );
		};
		LinkData.getTriplesByProperty( topWorkId, topFileName, topProperty, getTriplesByProperty, index.getIndex() );
	},

_showMotifByTripleList : function( workId, fileName, property, tripleList ) {
		var self = this, i = 0, subject = tripleList [ i ].object;
		var cnt = 0;
		var subjects = [];
		var posProperty = self._motifProperty.getPropertyByLabel( self._options.motifPositionProperty );
		var showMotif = function( posTripleList ) {
			var found = false;
			i++;
			$.each( posTripleList, function( pKey, pValue ) {
				var tmpPos = parseInt( pValue, 10 );
				// モチーフの位置がベース配列の範囲内に収まっていれば
				if( self._options.baseSequenceMinLength < tmpPos && self._options.baseSequence.length >= tmpPos )
				{
					// 発見のフラグを立てる。
					found = true;
					return false;
				}
			} );
			if( found )
			{
				var j;
				// 適合するモチーフをランキングのための配列に追加
				for( j = 0; j < cnt; j++ )
				{
					if( subject === subjects[ j ] )
					{
						break;
					}
				}
				if( j === cnt )
				{
					subjects[ cnt++ ] = subject;
				}
			}
			
			if( cnt < self._options.rankingRange )
			{
				// 次のtripleへ。
				subject = tripleList[ i ].object;
				LinkData.getObjects( workId, fileName, subject, posProperty, showMotif );
			}
			else
			{
				// 規定数の遺伝子が集まった場合はランキング生成へ
				self._showRanking( subjects );
			}
		};
		LinkData.getObjects( workId, fileName, subject, posProperty, showMotif );
	},
	
	_getDataBaseWebsiteName : function() {
		var self = this;
		var fileName = self._options.fileName;
		var rtnVal;
		if( fileName.indexOf( self._options.websiteNameAtted ) > -1 )
		{
			rtnVal = self._options.websiteNameAtted;
		}
		else if( fileName.indexOf( self._options.websiteNamePpdb ) > -1 )
		{
			rtnVal = self._options.websiteNamePpdb;
		}
		else
		{
			rtnVal = "UNKNOWN";
		}
		return rtnVal;
	},
	
	_motifSequence : function( workId, fileName, subject, property ) {
		var self = this;
		var drawSequence = function( seqHtml ) {
			var sb = [];
			sb[sb.length] = "<input type='hidden' class='" + self._default.geneLabelClass + "' value='" + subject + "'/>";
			sb[sb.length] = "<div class='baseSequence'>" + self._baseSequence + "</div>";
			sb[sb.length] = seqHtml;
			$( "#" + self._containerId + " ." + self._options.resultAreaClass ).html( sb.join( "" ) );
			if( seqHtml.length === 0 )
			{
				$( "#" + self._containerId + " ." + self._options.replaceButtonAreaClass ).hide();
			}
			self._initMotifSequenceListener();
			self._initReplaceButtonLitener();
			self._showDataBaseInformationList();
			self._showGenePlot( subject, property );
			$( "#" + self._containerId + " ." + self._options.resultAreaClass ).show();
			$( "#" + self._containerId + " ." + self._options.replaceButtonAreaClass ).show();
			$( "#" + self._containerId + " ." + self._options.loadingImageContainer ).hide();
		};
		self._appSequence.getSequenceHtml( subject, drawSequence );
	},
	
	_getMinPosition : function( seq ) {
		var self = this;
		var mod = seq.length % 2;
		var tHold = ( mod === 1 ) ? 1 : 0.5;
		return self._default.baseSequenceMinLength + Math.floor( seq.length / 2 ) + tHold;
	},
	
	_getMaxPosition : function( seq ) {
		var self = this;
		var mod = seq.length % 2;
		var tHold = (mod === 1) ? 0 : 0.5;
		return self._baseSequence.length - 1 - Math.floor( seq.length / 2 ) + tHold;
	},
	
	_getSeqElBySeq : function( seq ) {
		var rtnVal;
		if( seq && seq.trim().length === 7 )
		{
			rtnVal = this._heptamer.getBySequence( seq );
		}
		else if( seq && seq.trim().length === 8 )
		{
			rtnVal = this._octamer.getBySequence( seq );
		}
		return rtnVal;
	},
	
	_showDatabaseInfo : function( seqVal )
	{
		var self = this, fileName = self._options.fileName, appName = self._options.appName;
		var propLabel = $( "option:selected", "#" + self._containerId + " ." + self._options.selectPropertyClass ).val();
		var subject = $( "#" + self._containerId + " ." + self._options.geneLabelClass ).val();
		// TopかBottomか。
		var order = $( "#" + self._containerId + " [name=" + self._options.selectOrderName + "]:checked" ).val();
		// コンボボックスの何個目か = 順位
		var rank = $( "#" + self._containerId + " ." + self._options.selectRankingClass ).find( "option:selected" ).index();
		var label = self._motifProperty._getDisplayLabel( propLabel );
		label = ( label && label.trim().length !== 0 ) ? label : propLabel;
		var usedMotif = ( seqVal.length !== 0 ) ? seqVal : "-";
		var dbInfoHtml = self._getDatabaseInfo( fileName, appName, subject, label, usedMotif, order, rank );
		$( "#" + self._containerId + " ." + self._options.databaseInfoClass ).html( dbInfoHtml );
		$( "#" + self._containerId + " ." + self._options.databaseInfoClass ).show();
		self._genePreviewListener(subject);
	},
	
	_genePreviewListener : function( subject ) {
		var self = this;
		$( "#" + self._containerId + " ." + self._options.geneInfoLinkClass ).click( function() {
			self._showPopupWindow( subject );
		} );
	},
	
	_getDatabaseInfo : function( fileName, method, subject, property, motif, order, rank ) {
		var self = this;
		var gene = self._motifProperty.getGeneBySubject( subject );
		var sb = [];
		sb[ sb.length ] = "<div class='row'>";
		sb[ sb.length ] = "<div class='label left'>Database</div>";
		sb[ sb.length ] = "<div class='left'>" + fileName + "</div>";
		sb[ sb.length ] = "</div>";
		sb[ sb.length ] = "<div class='row'>";
		sb[ sb.length ] = "<div class='label left'>Application</div>";
		sb[ sb.length ] = "<div class='left'>" + method + "</div>";
		sb[ sb.length ] = "</div>";
		sb[ sb.length ] = "<div class='row'>";
		sb[ sb.length ] = "<div class='label left'>Rank </div>";
		sb[ sb.length ] = "<div class='left'>" + ( ( order === self._options.topValue ) ? "Top" : "Bottom" ) + "&nbsp;" + rank + "</div>";
		sb[ sb.length ] = "</div>";
		sb[ sb.length ] = "<div class='row'>";
		sb[ sb.length ] = "<div class='label left'>Gene Locus</div>";
		sb[ sb.length ] = "<div class='left'>";
		sb[ sb.length ] = "<a href='javascript:void(0);' class='" + self._options.geneInfoLinkClass + "'>" + gene + "</a>";
		sb[ sb.length ] = "</div>";
		sb[ sb.length ] = "</div>";
		sb[ sb.length ] = "<div class='row'>";
		sb[ sb.length ] = "<div class='label left'>Property</div>";
		sb[ sb.length ] = "<div class='left'>" + property + "</div>";
		sb[ sb.length ] = "</div>";
		sb[ sb.length ] = "<div class='row'>";
		sb[ sb.length ] = "<div class='label left'>Motif</div>";
		sb[ sb.length ] = "<div class='left motif'>" + motif + "</div>";
		sb[ sb.length ] = "</div>";
		return sb.join( "" );
	},
	
	_replaceWithSequence : function( seq, pos, extraCopies, basePairs ) {
		var self = this;
		var html = self._appSequence.replaceWith( seq, pos, extraCopies, basePairs );
		$( "#" + self._containerId + " ." + self._options.replaceSequenceClass ).html( html );
		$( "#" + self._containerId + " ." + self._options.replaceSequenceClass ).show();
		var seqLabel = seq + "[" + pos + "]";
		self._showDatabaseInfo( seqLabel );
		self._options.callback();
	}
	
};

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

Application.geneChart.prototype = {
	
	_containerId : null,
	_options : null,
	_workId : null,
	_fileName : null,
	_subject : null,
	_property : null,
	_highChartContainerId : null,
	_appProperty : null,
	
	_default : {
		filterNamespace : "http://linkdata.org/",
		acceptPropLabelPrefix : "label:"
	},
	
	_init : function( containerId, options ) {
		this._containerId = containerId;
		this._options = $.extend( {}, this._default, options );
		this._workId = this._options.workId;
		this._fileName = this._options.fileName;
		this._subject = this._options.subject;
		this._property = this._options.property;
		var date = new Date();
		this._highChartContainerId = "gene_chart_" + date.getTime();
		this._initAppProperty( this._options );
		this._initView();
		this._drawHighChart( this._subject, this._property );
	},
	
	_initAppProperty : function( opts ) {
		var obj = {
			workId : opts.workId,
			fileName : opts.fileName
		};
		this._appProperty = new Application.motifProperty( obj );
	},
	
	_initView : function() {
		var self = this;
		var sb = [];
		sb[ sb.length ] = "<div id='" + self._highChartContainerId + "'></div>";
		$( "#" + self._containerId ).html( sb.join( "" ) );
	},
	
	_ignore : function( label ) {
		var self = this;
		if( label.indexOf( self._default.acceptPropLabelPrefix ) > -1 )
		{
			return false;
		}
		return true;
	},
	
	_getDisplayLabel : function( value ) {
		var self = this;
		var propLabel = value;
		var arr = value.split( self._default.acceptPropLabelPrefix );
		if( arr.length > 1 )
		{
			propLabel = decodeURIComponent( arr[  1] );
		}
		return propLabel;
	},
	
	_drawHighChart : function( subject, highlightProperty ) {
		var self = this;
		var getDataArray = function( tripleList ) {
			var dataArray = [];
			var dataObject = {};
			var array = [];
			var duplicateProperty = [];
			$.each (tripleList, function( tKey, tValue ) {
				var property = tValue.property;
				if( property.indexOf( self._options.filterNamespace ) === -1 )
				{
					return;
				}
				if( $.inArray( property, duplicateProperty ) > -1 )
				{
					return;
				}
				var label = self._getLabelAfterHash( property );
				if( !self._ignore( label ) )
				{
					var val = parseFloat( tValue.object );
					if( highlightProperty === property )
					{
						val = self._getHighLightColumn( parseFloat( tValue.object ) );
					}
					array.push( val );
					duplicateProperty.push( property );
				}
			} );
			dataObject.name = self._getLabel( subject );
			dataObject.data = array;
			dataArray.push( dataObject );
			self._getXCategory( tripleList, dataArray, highlightProperty );
		};
		LinkData.getTriplesBySubject( self._workId, self._fileName, subject, getDataArray );
	},
	
	_getXCategory : function( tripleList, dataArray, highlightProperty ) {
		var self = this;
		var array = [];
		var duplicateProperty = [];
		var hLabel = self._getLabelAfterHash( highlightProperty );
		$.each ( tripleList, function( tKey, tValue ) {
			var property = tValue.property;
			if( property.indexOf( self._options.filterNamespace ) === -1 )
			{
				return;
			}
			if( $.inArray( property, duplicateProperty ) > -1 )
			{
				return;
			}
			var label = self._getLabelAfterHash( property );
			if( !self._ignore( label ) )
			{
				var displayLabel = self._getDisplayLabel( label );
				var hDisplayLabel = self._getDisplayLabel( hLabel );
				if( displayLabel === hDisplayLabel )
				{
					displayLabel = "<span style=\"color:#FB3B44\">" + hDisplayLabel + "</span>";
				}
				array.push( displayLabel );
				duplicateProperty.push( property );
			}
		} );
		self._drawChart( self._highChartContainerId, dataArray, array );
	},
	
	_getHighLightColumn : function( val ) {
		var obj = {};
		obj.y = val;
		obj.marker = {
			lineWidth: 3,
			lineColor: "#FB3B44",
			fillColor: "#FB3B44"
		};
		return obj;
	},
	
	_drawChart : function( containerId, dataArray, xCategory ) {
		var self = this;
		var chart = new Highcharts.Chart( {
			chart: {
				renderTo: containerId,
				type: 'line',
				marginRight: 130,
				marginBottom: 125
			},
			title: {
				text: self._fileName
			},
			xAxis: {
				categories: xCategory,
				labels : {
					rotation: 315
				}
			},
			tooltip: {
				formatter: function() {
					return '<b>'+ this.series.name + '</b><br/>' + this.x + ' [' + this.y + ']';
				}
			},
			legend: {
				layout: 'vertical',
				align: 'right',
				verticalAlign: 'top',
				x: -10,
				y: 100,
				borderWidth: 0
			},
			series: dataArray
		} );
	},
	
	_getLabel : function( value ) {
		var self = this, label;
		if( value.indexOf( "#" ) > -1 )
		{
			label = self._getLabelAfterHash( value );
		}
		else
		{
			label = self._appProperty.getGeneBySubject( value );
		}
		if( !label )
		{
			label = value;
		}
		return label;
	},
	
	_getPropertyLabel : function( value ) {
		var propLabel = value;
		var arr = value.split( "#" );
		if( arr.length > 1 )
		{
			propLabel = decodeURIComponent( arr[ 1 ] );
			propLabel = this._appProperty.getPropertyNameByLabel( propLabel );
		}
		return propLabel;
	},
	
	_getLabelAfterHash : function( value ) {
		var propLabel = value;
		var arr = value.split( "#" );
		if( arr.length > 1 )
		{
			propLabel = decodeURIComponent( arr[ 1 ] );
		}
		return propLabel;
	}
	
};

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

Application.motifProperty.prototype = {

_options : null,
	_propMap : null,
	_nameMap : null,
	_optionArray : null,
	
	_default : {
		acceptPropLabelPrefix : "label:",
		subjectATTEDUriPhrase : "http://atted.jp/data/locus/",
		subjectPPDBUriPhrase : "http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/display.cgi?organism=At&gene="
	},
	
	_init : function( options ) {
		this._options = $.extend( {}, this._default, options );
		this._propMap = [];
		this._nameMap = [];
		this._initPropMap( this._options );
	},
	
	_initPropMap : function( opts ) {
		var self = this, workId = opts.workId, fileName = opts.fileName;
		var method = function( properties ) {
			self._fillPropMap( self, properties );
			self._initOptionArray( properties );
		};
		LinkData.getProperties( workId, fileName, method );
	},
	
	_fillPropMap : function( self, properties ) {
		$.each( properties, function( key, value ) {
			var label = self._getLabel( value );
			if( !self._propMap[ label ] )
			{
				self._propMap[ label ] = value;
			}
		} );
	},
	
	_initOptionArray : function( propertyList ) {
		var self = this, list = {};
		var workId = self._options.workId, fileName = self._options.fileName;
		self._optionArray = [];
		$.each(propertyList, function( key, value ) {
			var propLabel = self._getLabel( value );
			if( !self._ignore( propLabel ) )
			{
				var obj = {};
				obj.key = propLabel;
				obj.value = self._getDisplayLabel( propLabel );
				self._optionArray.push( obj );
			}
		} );
	},
	
	_ignore : function (label ) {
		var self = this;
		if( label.indexOf( self._default.acceptPropLabelPrefix ) > -1 )
		{
			return false;
		}
		return true;
	},
	
	_getDisplayLabel : function( value ) {
		var self = this;
		var propLabel = value;
		var arr = value.split( self._default.acceptPropLabelPrefix );
		if( arr.length > 1 )
		{
			propLabel = decodeURIComponent( arr[ 1 ] );
		}
		return propLabel;
	},
	
	_getLabel : function( value ) {
		var propLabel = value;
		var arr = value.split( "#" );
		if( arr.length > 1 )
		{
			propLabel = decodeURIComponent( arr[ 1 ] );
		}
		return propLabel;
	},

getOptionArray : function() {
		return this._optionArray;
	},
	
	getPropertyByLabel : function( label ) {
		return this._propMap[ label ];
	},
	
	getGeneBySubject : function( subject ) {
		var self = this, htmlExt = ".html", geneLabel;
		if( subject.indexOf( self._default.subjectATTEDUriPhrase ) > -1 )
		{
			geneLabel = subject.replace( self._default.subjectATTEDUriPhrase, "" );
		}
		else if( subject.indexOf( self._default.subjectPPDBUriPhrase ) > -1 )
		{
			geneLabel = subject.replace( self._default.subjectPPDBUriPhrase, "" );
		}
		if( geneLabel && geneLabel.indexOf( htmlExt ) > -1 )
		{
			geneLabel = geneLabel.replace( htmlExt, "" );
		}
		return geneLabel;
	}
	
};

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

Application.sequence.prototype = {
	
	CHAR_SEQ_EMPTY : "-",
	
	_options : null,
	_workId : null,
	_fileName : null,
	_seqProperty : null,
	_posProperty : null,
	_baseSequence : null,
	_sequenceList : null,
	_positionList : null,
	_containerId : null,
	_errorContainerClass : null,
	_outOfRangeArray : null,
	
	_default : {
		msgInvalidSequence: "invalid sequence.",
		msgOutOfRangeSequence: "out of range sequence : {0}"
	},
	
	_init : function( options ) {
		this._options = options;
		this._workId = this._options.workId;
		this._fileName = this._options.fileName;
		this._seqProperty = this._options.motifSequenceProperty;
		this._posProperty = this._options.motifPositionProperty;
		this._baseSequence = this._options.baseSequence;
		this._containerId = this._options.containerId;
		this._errorContainerClass = this._options.errorMessageClass;
	},
	
	_getCustomSequenceHtml : function( baseSequence, sequence, position ) {
		var i;
		var seqLen = sequence.length;
		var tHold = Math.floor( seqLen / 2 ) + 1;
		var pos = parseInt( position, 10 );
		var baseSeqLen = baseSequence.length;
		var suffixLen = baseSeqLen - tHold - pos;
		var sb = [];
		if( pos > this._options.baseSequenceMinLength && suffixLen > 0) {
			for( i = 0; i < suffixLen; i++ )
			{
				sb.push( this.CHAR_SEQ_EMPTY );
			}
			sb.push( "<a href='javascript:void(0)' class='motifSequence'>" + sequence + "</a>" );
			sb.push( "<input type='hidden' class='hdnSequence' value='" + sequence + "'/>" );
			sb.push( "<input type='hidden' class='hdnPosition' value='" + pos + "'/>" );
		}
		else
		{
			//_showError($appContainer, opts.msgOutOfRangeSequence.replace( "{0}", sequence ) );
			this._outOfRangeArray.push( sequence + "[" + pos + "]" );
			this._showError( this._default.msgOutOfRangeSequence.replace( "{0}", this._outOfRangeArray.join( ", " ) ) );
		}
		return sb.join( "" );
	},
	
	_isValidSequenceList : function( seqs ) {
		var i;
		var count = seqs.length;
		var maxlength = 0;
		for( i = 0; i < count; i++ )
		{
			if( seqs[ i ].length > maxlength )
			{
				maxlength = seqs[ i ].length;
			}
		}
		var result = true;
		for( i = 0; i < maxlength; i++ )
		{
			var j;
			var chars = [];
			for( j = 0; j < count; j++ )
			{
				chars.push( seqs[ j ].charAt( i ) );
			}
			if( !this._isValidChars( chars.join( "" ) ) )
			{
				result = false;
				break;
			}
		}
		return result;
	},
	
	_isValidChars : function( charString ) {
		var i;
		var charLen = charString.length;
		var result = true;
		var first = null;
		for( i = 0; i < charLen; i++)
		{
			if( charString.charAt( i ) !== this.CHAR_SEQ_EMPTY )
			{
				if( !first )
				{
					first = charString.charAt( i );
				}
				var current = charString.charAt( i );
				if( current && first !== current )
				{
					result = false;
					break;
				}
			}
		}
		return result;
	},
	
	_getReplacedCustomSequence : function( seqs ) {
		var i;
		var mergeSequence = this._getmergeCharSequence( seqs );
		var maxlength = this._baseSequence.length;
		var sb = [];
		for( i = 0; i < maxlength; i++ )
		{
			var bChar = this._baseSequence.charAt( i );
			var mChar = mergeSequence.charAt( i );
			if( mChar !== this.CHAR_SEQ_EMPTY )
			{
				// replaced
				sb.push( mChar );
			}
			else
			{
				sb.push( bChar );
			}
		}
		
		return sb.join( "" );
	},
	
	_getmergeCharSequence : function( seqs ) {
		var i;
		var count = seqs.length;
		var maxlength = this._baseSequence.length;
		var sb = [];
		for( i = 0; i < maxlength; i++ )
		{
			var j;
			var chars = [];
			for( j = 0; j < count; j++ )
			{
				chars.push( seqs[ j ].charAt( i ) || this.CHAR_SEQ_EMPTY );
			}
			sb.push( this._getMergeChar( chars.join( "" ) ) );
		}
		return sb.join( "" );
	},
	
	_getMergeChar : function( charString ) {
		var i;
		var charLen = charString.length;
		var result = null;
		for( i = 0; i < charLen; i++ )
		{
			if( charString.charAt( i ) !== this.CHAR_SEQ_EMPTY )
			{
				result = charString.charAt( i );
				break;
			}
		}
		if( !result )
		{
			result = this.CHAR_SEQ_EMPTY;
		}
		return result;
	},
	
	_wrappedReplacedSequenceHtml : function( replaceSequence, seqs ) {
		var i;
		var mergeSequence = this._getmergeCharSequence( seqs );
		var length = this._baseSequence.length;
		var sb = [];
		for( i = 0; i < length; i++ )
		{
			var bChar = this._baseSequence.charAt( i );
			var rChar = replaceSequence.charAt( i );
			var mChar = mergeSequence.charAt( i );
			var seqChar = ( bChar !== rChar ) ? "<span class='replace'>" + rChar + "</span>" : rChar;
			if( mChar !== this.CHAR_SEQ_EMPTY )
			{
				sb.push( "<span class='highlight-sequence'>" + seqChar + "</span>" );
			}
			else
			{
				sb.push( seqChar );
			}
		}
		return sb.join( "" );
	},
	
	_showError : function( message ) {
		$errorMessageContainer = $( "#" + this._containerId + " ." + this._errorContainerClass );
		$errorMessageContainer.html( message );
		$errorMessageContainer.show();
	},
	
	getSequenceHtml : function( subject, drawSequence ) {
		var self = this;
		self._outOfRangeArray = [];
		var sb = [], baseSequence = self._baseSequence;
		var getTriplesBySequenceProperty = function( sequenceList ) {
			self._getTriplesBySequenceProperty( subject, drawSequence, sequenceList );
		};
		LinkData.getObjects( self._workId, self._fileName, subject, self._seqProperty, getTriplesBySequenceProperty );
	},
	
	_getTriplesBySequenceProperty : function( subject, drawSequence, sequenceList ) {
		var self = this;
		var getTriplesByPositionProperty = function( positionList ) {
			self._drawSequenceList( drawSequence, sequenceList, positionList );
		};
		LinkData.getObjects( self._workId, self._fileName, subject, self._posProperty, getTriplesByPositionProperty );
	},
	
	_drawSequenceList : function( drawSequence, sequenceList, positionList ) {
		var i;
		var self = this, sb = [];
		if( !sequenceList || sequenceList.length === 0) {
			return;
		}
		for( i = 0; i < sequenceList.length; i++ ) {
			var customSeqString = self._getCustomSequenceHtml( self._baseSequence, sequenceList[ i ], positionList[ i ] );
			if( customSeqString.length > 0 )
			{
				sb.push( "<div class='userSequence'>" + customSeqString + "</div>" );
			}
		}
		drawSequence( sb.join( "\n" ) );
	},
	
	replace : function( seqs ) {
		var isValid = this._isValidSequenceList( seqs );
		if( isValid )
		{
			if( seqs.length > 0 )
			{
				var replaceSeq = this._getReplacedCustomSequence( seqs );
				var replaceSeqHtml = this._wrappedReplacedSequenceHtml( replaceSeq, seqs );
				return replaceSeqHtml;
			}
		}
		else
		{
			this._showError( this._default.msgInvalidSequence );
		}
	},
	
	replaceWith : function( seq, pos, extraCopies, basePairs ) {
		var j;
		var main = [];
		var seqLen = seq.length;
		var tHold = Math.floor( seqLen / 2 ) + 1;
		pos = parseInt( pos, 10 );
		var baseSeqLen = this._baseSequence.length;
		var len = baseSeqLen - tHold - pos;
		for( j = 0; j < extraCopies + 1; j++ )
		{
			var i;
			var array = [];
			for( i = 0; i < len; i++ )
			{
				array.push( this.CHAR_SEQ_EMPTY );
			}
			array.push( seq );
			main.push( array.join( "" ) );
			len = len - seqLen - basePairs;
			if( len < 0 )
			{
				break;
			}
		}
		return this.replace( main );
	},
	
	hideError : function() {
		$errorMessageContainer = $( "#" + this._containerId + " ." + this._errorContainerClass ).hide();
	}
	
};

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

Application.heptamer.prototype = {
	
	_heptamerMap : null,
	_motifSequenceProperty : null,
	_appropriatePositionProperty : null,
	
	_default : {
		heptamerTag : "heptamer",
		filterSequencePropertyPhrase : "motif_sequence",
		filterMaxCEGPropertyPhrase : "maxCEG",
		filterAppropriatePosition : "Appropriateposition(%C2%B1%2040%20bp)"
	},
	
	_init : function() {
		this._heptamerMap = [];
		this._initHeptamerList();
	},
	
	_initHeptamerList : function() {
		var self = this;
		var getFilesByTag = function( result ) {
			$.each(result, function( workId, fileList ) {
				$.each(fileList, function( fileKey, fileName ) {
					self._initHeptamer( workId, fileName );
					return false;
				} );
			} );
		};
		LinkData.getFilesByTag( null, self._default.heptamerTag, getFilesByTag );
	},
	
	_initHeptamer : function( workId, fileName ) {
		var self = this;
		var getPropertyList = function( propertyList ) {
			self._initProperty( propertyList );
			self._getSequenceTriple( workId, fileName );
		};
		LinkData.getProperties( workId, fileName, getPropertyList );
	},
	
	_initProperty : function( propertyList ) {
		var self = this;
		$.each(propertyList, function( propKey, propValue ) {
			if( propValue.indexOf(self._default.filterSequencePropertyPhrase) > -1 )
			{
				self._motifSequenceProperty = propValue;
			}
			else if( propValue.indexOf( self._default.filterAppropriatePosition ) > -1 )
			{
				self._appropriatePositionProperty = propValue;
			}
		} );
	},
	
	_getSequenceTriple : function( workId, fileName ) {
		var self = this;
		var getSequenceTripleList = function( sequenceTripleList ) {
			self._fillHeptamerMap( workId, fileName, sequenceTripleList );
		};
		LinkData.getTriplesByProperty( workId, fileName, self._motifSequenceProperty, getSequenceTripleList );
	},
	
	_fillHeptamerMap : function( workId, fileName, sequenceTripleList ) {
		var i;
		var self = this;
		var getPositionTripleList = function( positionTripleList ) {
			for( i = 0; i < sequenceTripleList.length; i++ )
			{
				var seqTriple = sequenceTripleList[ i ];
				var posTriple = positionTripleList[ i ];
				var seqEl = new Application.seqElement();
				seqEl.setExternalUrl( seqTriple.subject );
				seqEl.setSequence( seqTriple.object );
				seqEl.setAppropriatePos( posTriple.object );
				self._heptamerMap[ seqTriple.object ] = seqEl;
			}
		};
		LinkData.getTriplesByProperty( workId, fileName, self._appropriatePositionProperty, getPositionTripleList );
	},
	
	getBySequence : function( sequence ) {
		return this._heptamerMap[ sequence ];
	}
	
};

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

Application.octamer.prototype = {
	
	_octamerMap : null,
	_motifSequenceProperty : null,
	_appropriatePositionProperty : null,
	
	_default : {
		octamerTag : "octamer",
		filterSequencePropertyPhrase : "sequence",
		filterAppropriatePosition : "Appropriate%20position"
	},
	
	_init : function() {
		this._octamerMap = [];
		this._initOctamerList();
	},
	
	_initOctamerList : function() {
		var self = this;
		var getFilesByTag = function( result ) {
			$.each( result, function( workId, fileList ) {
				$.each(fileList, function( fileKey, fileName ) {
					self._initOctamer( workId, fileName );
					return false;
				} );
			} );
		};
		LinkData.getFilesByTag( null, self._default.octamerTag, getFilesByTag );
	},
	
	_initOctamer : function( workId, fileName ) {
		var self = this;
		var getProperties = function( propertyList ) {
			self._initProperty( propertyList );
			self._getSequenceTriple( workId, fileName );
		};
		LinkData.getProperties( workId, fileName, getProperties );
	},
	
	_initProperty : function( propertyList ) {
		var self = this;
		$.each( propertyList, function( propKey, propValue) {
			if( propValue.indexOf( self._default.filterSequencePropertyPhrase ) > -1 )
			{
				self._motifSequenceProperty = propValue;
			}
			else if( propValue.indexOf( self._default.filterAppropriatePosition ) > -1 )
			{
				self._appropriatePositionProperty = propValue;
			}
		} );
	},
	
	_getSequenceTriple : function( workId, fileName ) {
		var self = this;
		var getSequenceTripleList = function( sequenceTripleList ) {
			self._fillOctamerMap( workId, fileName, sequenceTripleList );
		};
		LinkData.getTriplesByProperty( workId, fileName, self._motifSequenceProperty, getSequenceTripleList );
	},
	
	_fillOctamerMap : function( workId, fileName, sequenceTripleList ) {
		var i;
		var self = this;
		var getPositionTripleList = function( positionTripleList ) {
			for( i = 0; i < sequenceTripleList.length; i++ )
			{
				var j = Math.floor( i / 2 );
				var seqTriple = sequenceTripleList[ i ];
				var posTriple = positionTripleList[ j ];
				var seqEl = new Application.seqElement();
				seqEl.setExternalUrl( seqTriple.subject );
				seqEl.setSequence( seqTriple.object );
				seqEl.setAppropriatePos( posTriple.object );
				self._octamerMap[ seqTriple.object ] = seqEl;
			}
		};
		LinkData.getTriplesByProperty( workId, fileName, self._appropriatePositionProperty, getPositionTripleList );
	},
	
	getBySequence : function( sequence ) {
		return this._octamerMap[ sequence ];
	}
	
};

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

Application.seqElement.prototype = {
	
	_externalUrl : null,
	_sequence : null,
	_appropriatePos : null,
	
	_init : function() {},
	
	getExternalUrl : function() {
		return this._externalUrl;
	},

setExternalUrl : function( externalUrl ) {
		this._externalUrl = externalUrl;
	},
	
	getSequence : function() {
		return this._sequence;
	},
	
	setSequence : function( sequence ) {
		this._sequence = sequence;
	},
	
	getAppropriatePos : function() {
		return this._appropriatePos;
	},
	
	setAppropriatePos : function( appropriatePos ) {
		this._appropriatePos = appropriatePos;
	}
	
};

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++;
	}
};

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;
	}
	
};

$(document).ready(function() {
	var fillDatabase = function( resultList ) {
		$( ".motifRankingDatabase" ).append( "<option value='-1' selected='selected'>-- Select Database --</option>" );
		$.each( resultList, function( workId, fileList ) {
			$.each( fileList, function( fileKey, fileName ) {
				$( ".motifRankingDatabase" ).append( "<option value='" + workId + "|" + fileName + "'>" + fileName + "</option>" );
			} );
		 } );
		$( ".motifRankingDatabase " ).change( function() {
			var dbKey = $( "option:selected", $( this ) ).val();
			if( dbKey === -1 ) {
				$( "#container" ).html( "" );
				return;
			}
			var array = dbKey.split( "|" );
			var containerId = "container";
			var options = {
				workId : array[ 0 ],
				fileName : array[ 1 ],
				baseSequence : "GAAAAAAGACGTTCCAACCACGTCTTCAAAGCAAGTGATTGGATTAAGGTTCTTCCACACGGTAAGGGATGGCACTAACACCTACCATCCTTCGCAAGACCCTTCCTCTATATAAGGAAGTTCATTTCATTTGGAGAGGACCTCGAC"
			};
			var app = new Application.motifRanking( containerId, options );
		} );
	};
	LinkData.getFilesByTag( null, "database", fillDatabase );
} );

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

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

.hidden {
	display:none;
}

.left {
    float: left;
}

.label {
	color: #E87B10;
    font: 1.1em "Trebuchet MS","Helvetica","Arial","Verdana","sans-serif";
    height: 24px;
    min-width: 125px;
}

.row {
    padding: 5px 0;
}

.row:after {
    content: "";
    clear: left;
    display: block;
}

.row input[type="text"] {
    width: 200px;
}

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

.replace {
    color: #E80010;
}

.errorMessage {
	color: #FF0000;
	text-align: center;
}

.databaseInfo .motif {
	width: 70%;
}

/**
 * button css
 */
.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;
}

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

.motifViewDialog .basePairs,
.motifViewDialog .extraCopies,
.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;
}

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Circadian Coexpression (DIURNAL + ATTED-II promoter motif) Full Contributor:GenoCon Update:Jan 15, 2013 3470 Downloads, 27 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> Captions for properties of data tables: </b> <table style="text-align:left;"> <tr> <th nowrap> motif position </th> <td> The distance from the center base pair to the transcription start site. </td> </tr> <tr> <th nowrap> motif </th> <td> A link to the database page for the given cis-regulatory motif. </td> </tr> <tr> <th nowrap> motif sequence </th> <td> The sequence of the cis-regulatory motif. </td> </tr> <tr> <th nowrap> CEG </th> <td> The Coexpression Expression Group score as calculated by ATTED-II. </td> </tr> <tr> <th nowrap> Probe Condition </th> <td> The strain and growth condition of the 44 hour experiment. </td> </tr> <tr> <th nowrap> Phase </th> <td> The phase of circadian response, calculated by sine wave fitting. </td> </tr> <tr> <th nowrap> Correlation </th> <td> The correlation coefficient of the fitted sine wave with the circadian oscillation. </td> </tr> <tr> <th> label:Expression X hours </th> <td> The gene expression level after the seedling has been growing for X hours, starting at 7 days. </td> </tr> </table> <br> <br> --> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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/rdf1s330i/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 [database] DiurnalHours_ATTED_COL_SD [database] DiurnalHours_ATTED_DD_DDHC [database] DiurnalHours_ATTED_LDHC [database] DiurnalHours_ATTED_LDHH_SM [database] DiurnalHours_ATTED_LDHH_ST [database] DiurnalHours_ATTED_LER_SD [database] DiurnalHours_ATTED_LIGHT5_HIF138_13 [database] DiurnalHours_ATTED_LIGHT5_HIF138_8 [database] DiurnalHours_ATTED_LIGHT5_znknOX [database] DiurnalHours_ATTED_LL12_LDHH [database] DiurnalHours_ATTED_LL23_LDHH [database] DiurnalHours_ATTED_LLHC [database] DiurnalHours_ATTED_LL_LDHC [database] DiurnalHours_ATTED_LL_LLHC [database] DiurnalHours_ATTED_lhyox_SD [database] DiurnalHours_ATTED_longday [database] DiurnalHours_ATTED_lux_2_LDHH [database] DiurnalHours_ATTED_phyB9_SD [database] DiurnalHours_ATTED_shortday [database]
Circadian Genomic (DIURNAL + PPDB promoter motif) Full Contributor:GenoCon Update:Jan 15, 2013 3369 Downloads, 29 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> Captions for properties of data tables: </b> <table style='text-align:left;'> <tr> <th nowrap> PPDB motif </th> <td> A link to the PPDB database page for the given cis-regulatory motif. </td> </tr> <tr> <th nowrap> motif type </th> <td> Type of the PPDB promoter motif. The identified octamers have been classified into regulatory element group (REG), TATA box, and Y Patch. </td> </tr> <tr> <th nowrap> motif sequence </th> <td> The sequence of the cis-regulatory motif. </td> </tr> <tr> <th nowrap> motif position </th> <td> The distance from the center base pair to the transcription start site (TSS). </td> </tr> <tr> <th nowrap> genome_version </th> <td> The genome version of annotated motifs. </td> </tr> <tr> <th nowrap> TAIR_gene </th> <td> Gene information associated with the motifs. </td> </tr> <tr> <th nowrap> chromosome </th> <td> Chromosome number the gene belongs. </td> </tr> <tr> <th nowrap> position start </th> <td> The absolute start position of the motif. </td> </tr> <tr> <th nowrap> position start from TSS peak </th> <td> The position of the motif start relative to the TSS peak. </td> </tr> <tr> <th nowrap> position end </th> <td> The absolute end position of the motif. </td> </tr> <tr> <th nowrap> position end from TSS peak </th> <td> The position of the motif end relative to the TSS peak. </td> </tr> <tr> <th nowrap> strand </th> <td> The strand of the feature. + for positive strand, - for minus strand. </td> </tr> <tr> <th nowrap> TSS peak position </th> <td> The absolute position of the TSS peak, which is the most probable TSS position determined by the CT-MPSS method. </td> </tr> <tr> <th> TSS peak position from Initial codon </th> <td> The position of the TSS peak relative to Initial codon. </td> </tr> <tr> <th nowrap> Initial codon </th> <td> The absolute position of the Initial codon. </td> </tr> <tr> <th nowrap> label:Expression X hours </th> <td> The gene expression level after the seedling has been growing for X hours, starting at 7 days. </td> </tr> </table> <br> <br> --> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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/rdf1s331i/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>	DiurnalHours_PPDB_COL_LDHH [database] DiurnalHours_PPDB_COL_SD [database] DiurnalHours_PPDB_DD_DDHC [database] DiurnalHours_PPDB_LDHC [database] DiurnalHours_PPDB_LDHH_SM [database] DiurnalHours_PPDB_LDHH_ST [database] DiurnalHours_PPDB_LER_SD [database] DiurnalHours_PPDB_LIGHT5_HIF138_13 [database] DiurnalHours_PPDB_LIGHT5_HIF138_8 [database] DiurnalHours_PPDB_LIGHT5_znknOX [database] DiurnalHours_PPDB_LL12_LDHH [database] DiurnalHours_PPDB_LL23_LDHH [database] DiurnalHours_PPDB_LLHC [database] DiurnalHours_PPDB_LL_LDHC [database] DiurnalHours_PPDB_LL_LLHC [database] DiurnalHours_PPDB_lhyox_SD [database] DiurnalHours_PPDB_longday [database] DiurnalHours_PPDB_lux_2_LDHH [database] DiurnalHours_PPDB_phyB9_SD [database] DiurnalHours_PPDB_shortday [database]
Developmental Coexpression (AtGenExpress + ATTED-II promoter motif) Full Contributor:GenoCon Update:Mar 6, 2013 2856 Downloads, 32 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> Captions for properties of data tables: </b> <table style='text-align:left;'> <tr> <th nowrap> label:Conditions </th> <td> The genes ranked by absolute expression level under the given growth conditions. </td> </tr> </table> <br> <br> --> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s328i/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/rdf1s328i/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/rdf1s328i/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/rdf1s328i/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/rdf1s328i/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/rdf1s328i/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/rdf1s328i/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> <tr> <td> <a href='http://linkdata.org/work/rdf1s328i/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 [database] AtGenExpress_ATTED_Fruit_Seeds [database] AtGenExpress_ATTED_Leaf [database] AtGenExpress_ATTED_Root [database] AtGenExpress_ATTED_Seedling [database] AtGenExpress_ATTED_Stem [database] AtGenExpress_ATTED_Whole_Plant [database] Heptamer_elements [heptamer] PPDB_position []
Speedup Lists of Developmental Genomic (AtGenExpress + PPDB promoter motif) Gene Contributor:GenoCon Update:Jan 15, 2013 824 Downloads, 21 Applications Lists for the AtGenExpress and PPDB mashup data table. For each experiment, the top 1000 and bottom 1000 genes ranked by absolute expression level. This also includes the full List for MotifQuery function. <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> Captions for properties of data tables: </b> <table style='text-align:left;'> <tr> <th nowrap> label:Conditions </th> <td> The genes ranked by absolute expression level under the given growth conditions. </td> </tr> </table> <br> <br> --> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s341i/AtGenExpress_PPDB_top.html#work_information'>AtGenExpress_PPDB_top</a> </td> <td> Lists for the AtGenExpress and PPDB (Plant Promoter Database) mashup data table. For each experiment, the top 1000 genes ranked by absolute expression level. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s341i/AtGenExpress_PPDB_bottom.html#work_information'>AtGenExpress_PPDB_bottom</a> </td> <td> Lists for the AtGenExpress and PPDB (Plant Promoter Database) mashup data table. For each experiment, the bottom 1000 genes ranked by absolute expression level. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s341i/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 absolute expression level. </td> </tr> </table>	AtGenExpress_PPDB_all [] AtGenExpress_PPDB_bottom [result_bottom] AtGenExpress_PPDB_top [result_top]
GenoCon2 Challenge A - Sequence Function Plugins Contributor:GenoCon Update:Nov 26, 2012 140 Downloads, 7 Applications	Application_Plugins_for_Synthetic_Promoter_Design [method]
Speedup Lists of Developmental Coexpression (AtGenExpress + ATTED-II promoter motif) Gene Contributor:GenoCon Update:Jan 15, 2013 861 Downloads, 24 Applications Lists for the AtGenExpress and ATTEDII mashup data table. For each experiment, the top 1000 and bottom 1000 genes ranked by absolute expression level. This also includes the full List for MotifQuery function. <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> Captions for properties of data tables: </b> <table style='text-align:left;'> <tr> <th nowrap> label:Conditions </th> <td> The genes ranked by absolute expression level under the given growth conditions. </td> </tr> </table> <br> <br> --> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s339i/AtGenExpress_ATTED_top.html#work_information'>AtGenExpress_ATTED_top</a> </td> <td> Lists for the AtGenExpress and ATTED-II mashup data table. For each experiment, the top 1000 genes ranked by absolute expression level. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s339i/AtGenExpress_ATTED_bottom.html#work_information'>AtGenExpress_ATTED_bottom</a> </td> <td> Lists for the AtGenExpress and ATTED-II mashup data table. For each experiment, the bottom 1000 genes ranked by absolute expression level. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s339i/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 absolute expression level. </td> </tr> </table>	AtGenExpress_ATTED_all [] AtGenExpress_ATTED_bottom [result_bottom] AtGenExpress_ATTED_top [result_top]
Developmental Genomic (AtGenExpress + PPDB promoter motif) Full Contributor:GenoCon Update:Jan 22, 2013 1763 Downloads, 27 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> Captions for properties of data tables: </b> <table style='text-align:left;'> <tr> <th nowrap> PPDB motif </th> <td> A link to the PPDB database page for the given cis-regulatory motif. </td> </tr> <tr> <th nowrap> motif type </th> <td> Type of the PPDB promoter motif. The identified octamers have been classified into regulatory element group (REG), TATA box, and Y Patch. </td> </tr> <tr> <th nowrap> motif sequence </th> <td> The sequence of the cis-regulatory motif. </td> </tr> <tr> <th nowrap> motif position </th> <td> The distance from the center base pair to the transcription start site (TSS). </td> </tr> <tr> <th nowrap> genome_version </th> <td> The genome version of annotated motifs. </td> </tr> <tr> <th nowrap> TAIR_gene </th> <td> Gene information associated with the motifs. </td> </tr> <tr> <th nowrap> chromosome </th> <td> Chromosome number the gene belongs. </td> </tr> <tr> <th nowrap> position start </th> <td> The absolute start position of the motif. </td> </tr> <tr> <th nowrap> position start from TSS peak </th> <td> The position of the motif start relative to the TSS peak. </td> </tr> <tr> <th nowrap> position end </th> <td> The absolute end position of the motif. </td> </tr> <tr> <th nowrap> position end from TSS peak </th> <td> The position of the motif end relative to the TSS peak. </td> </tr> <tr> <th nowrap> strand </th> <td> The strand of the feature. + for positive strand, - for minus strand. </td> </tr> <tr> <th nowrap> TSS peak position </th> <td> The absolute position of the TSS peak, which is the most probable TSS position determined by the CT-MPSS method. </td> </tr> <tr> <th> TSS peak position from Initial codon </th> <td> The position of the TSS peak relative to Initial codon. </td> </tr> <tr> <th nowrap> Initial codon </th> <td> The absolute position of the Initial codon. </td> </tr> <tr> <th nowrap> label:Conditions </th> <td> The gene expression level under the given growth conditions. </td> </tr> </table> <br> <br> --> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s329i/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/rdf1s329i/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/rdf1s329i/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/rdf1s329i/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/rdf1s329i/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/rdf1s329i/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/rdf1s329i/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> <tr> <td> <a href='http://linkdata.org/work/rdf1s329i/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>	AtGenExpress_PPDB_Flowering [database] AtGenExpress_PPDB_Fruit_Seeds [database] AtGenExpress_PPDB_Leaf [database] AtGenExpress_PPDB_Root [database] AtGenExpress_PPDB_Seedling [database] AtGenExpress_PPDB_Stem [database] AtGenExpress_PPDB_Whole_Plant [database] Octamer_elements [octamer]

Link http://app.linkdata.org/run/app1s135i?tab=readme