A Promoter Design to Maintain the Fertility of Transgenic Plant by New Plugin MotifRanking｜Mash up the Linked Open Data

about this App

A Promoter Design to Maintain the Fertility of Transgenic Plant by New Plugin MotifRanking

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

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

Application.genocon.prototype = {
	
	_baseSequence : null,
	_methodList : null,
	
	_default : {
		baseSequenceContainerId : "baseSequenceContainer",
		hiddenBaseSequenceClass : "hdnBaseSequence",
		fixedSequenceClass : "fixedSequence",
		baseErrorMessageClass : "baseErrorMessage",
		errorMessageEnterSequence : "Please enter a sequence of minimum length {0}",
		useButtonClass : "useButton",
		nextButtonClass : "nextButton",
		nextButtonContainerClass : "nextButtonContainer",
		collapseButton : "collapseButton",
		expandButton : "expandButton",
		removeButton : "removeButton",
		appContainerClass : "applicationContainer",
		appDataContainerClass : "applicationDataContainer",
		actionButtonContainer : "actionButtonContainer",
		actionResultContainer : "actionResultContainer",
		baseSequenceBoxClass : "baseSequenceBox",
		baseSequenceClass : "baseSequence",
		selectDataBaseList : "databaseList",
		selectMethodList : "optionList",
		hiddenBaseSequence : "hdnBaseSequence",
		databaseFilteringProperty : "#motif%20sequence",
		methodUrlProperty : "#application%20URL",
		baseSequenceMinLength : 50
	},
	
	_tag : {
		databaseTag : "database",
		methodTag : "method"
	},
	
	_init : function() {
		this._methodList = [];
		this._initBaseInput();
		this._initLoadScript();
		this._initDefaultContainer();
		this._initUseButtonListener();
	},
	
	_initBaseInput : function() {
		var val = $( "#" + this._default.baseSequenceContainerId + " ." + this._default.hiddenBaseSequenceClass ).val();
		if(val && val.length < this._default.baseSequenceMinLength) {
			$errMsgEl = $( "#" + this._default.baseSequenceContainerId + " ." + this._default.baseErrorMessageClass );
			$errMsgEl.html( self._default.errorMessageEnterSequence.replace( "{0}", self._default.baseSequenceMinLength ) );
			$errMsgEl.show();
			return;
		}
		$baseInput = $( "#" + this._default.baseSequenceContainerId + " ." + this._default.baseSequenceClass );
		var index = val.length - this._default.baseSequenceMinLength;
		$baseInput.attr( "size", index );
		var inputVal = val.substring( 0, index );
		var fixedVal = val.substring( index );
		$baseInput.val( inputVal );
		$( "#" + this._default.baseSequenceContainerId + " ." + this._default.fixedSequenceClass ).html( fixedVal );
		$baseInput.keyup( function() {
			var size = ( $baseInput.val().length !== 0 ) ? $baseInput.val().length : 1;
			$baseInput.attr( "size", size );
		} );
	},
	
	_initLoadScript : function() {
		var self = this;
		var getFilesByTag = function( result ) {
			$.each( result, function( workId, fileArray ) {
				$.each( fileArray, function( fileKey, fileName ) {
					var getProperties = function( propertytList ) {
						$.each( propertytList, function( propKey, propVal ) {
							if( propVal.indexOf( self._default.methodUrlProperty ) > -1 )
							{
								self._loadPluginScriptList( workId, fileName, propVal );
								return false;
							}
						 } );
					};
					LinkData.getProperties( workId, fileName, getProperties );
					return false;
				} );
			} );
		};
		LinkData.getFilesByTag( null, self._tag.methodTag, getFilesByTag );
	},
	
	_initDefaultContainer : function() {
		this._initDatabase();
		this._initMethod();
		this._initActionButton();
		this._initDatabaseListener();
		this._initMethodListener();
	},
	
	_initDatabase : function() {
		var self = this;
		var $select = $( "." + self._default.appContainerClass + " ." + self._default.selectDataBaseList );
		$( "option", $select).remove();
		$select.append( "<option value='-1' selected='selected'>-- Select Database --</option>" );
		var getFilesByTag = function( result ) {
			$.each(result, function( workId, fileArray ) {
				$.each( fileArray, function( fileKey, fileName ) {
					var dbKey = self._getDatabaseOptionKey( workId, fileName );
					$select.append( "<option value='" + dbKey + "'>" + fileName + "</option>" );
				} );
			} );
		};
		LinkData.getFilesByTag( "", self._tag.databaseTag, getFilesByTag );
	},
	
	_initMethod : function() {
		var self = this;
		var $select = $( "." + self._default.appContainerClass + " ." + self._default.selectMethodList );
		$( "option", $select).remove();
		$select.append( "<option value='-1' selected='selected'>-- Select Option --</option>" );
		var getFilesByTag = function( result ) {
			$.each( result, function( workId, fileArray ) {
				$.each( fileArray, function( fileKey, fileName ) {
					var getSubjects = function( subjectList ) {
						$.each( subjectList, function( subKey, subVal ) {
							var label = self._getLabel( subVal );
							$select.append( "<option value='" + label + "'>" + label + "</option>" );
							self._methodList.push( label );
						} );
					};
					LinkData.getSubjects( workId, fileName, getSubjects );
				} );
			} );
		};
		LinkData.getFilesByTag( null, self._tag.methodTag, getFilesByTag );
	},
	
	_initActionButton : function() {
		var self = this;
		$( "." + self._default.actionButtonContainer + " ." + self._default.collapseButton ).click( function() {
			var parent = $( this ).closest( "." + self._default.appContainerClass );
			$( parent ).find( "." + self._default.appDataContainerClass ).hide();
		} );
		$( "." + self._default.actionButtonContainer + " ." + self._default.expandButton ).click( function() {
			var parent = $( this ).closest( "." + self._default.appContainerClass );
			$( parent ).find( "." + self._default.appDataContainerClass ).show();
		} );
		$( "." + self._default.actionButtonContainer + " ." + self._default.removeButton ).click( function() {
			$( this ).closest( "." + self._default.appContainerClass ).remove();
		} );
	},
	
	_initDatabaseListener : function() {
		var self = this;
		
		var $selectDb = $( "." + self._default.appContainerClass + " ." + self._default.selectDataBaseList );
		$selectDb.change( function() {
			var parent = $( this ).closest( "." + self._default.appContainerClass );
			$( parent ).find( "." + self._default.nextButtonContainerClass ).hide();
			$container = $( parent ).find( "." + self._default.actionResultContainer );
			$container.html( "" );
			var dbKey = $( "option:selected", $( this ) ).val();
			self._changeMethodList( dbKey, parent );
		} );
	},
	
	_initMethodListener : function() {
		var self = this;
		var $selectDb = $( "." + self._default.appContainerClass + " ." + self._default.selectDataBaseList );
		var $select = $( "." + self._default.appContainerClass + " ." + self._default.selectMethodList );
		$select.change( function() {
			var parent = $( this ).closest( "." + self._default.appContainerClass );
			var method = $( "option:selected", $( this ) ).text();
			var database = $( "option:selected", $( parent ).find( "." + self._default.selectDataBaseList ) ).val();
			if( database === -1 )
			{
				return;
			}
			$container = $( parent ).find( "." + self._default.actionResultContainer );
			$container.html( "Loading..." );
			$( parent ).find( "." + self._default.nextButtonContainerClass ).hide();
			var date = new Date();
			var id = "container_id_" + date.getTime();
			$container.attr( "id", id );
			var func = function() {
				self._callback( self );
			};
			var arr = database.split( "|" );
			var obj = {
				workId : arr[ 0 ],
				fileName : arr[ 1 ],
				appName : method,
				baseSequence : self._baseSequence,
				callback : func
			};
			eval( method )( id, obj );
		} );
	},
	
	_loadPluginScriptList : function( workId, fileName, property ) {
		var getTripleList = function( tripleList ) {
			$.each( tripleList, function( tKey, tVal ) {
				LinkDataUtil.loadScript( tVal.object );
			} );
		};
		LinkData.getTriplesByProperty( workId, fileName, property, getTripleList );
	},
	
	_changeMethodList : function( dbKey, parent ) {
		var self = this;
		var $select = parent.find( "." + self._default.appContainerClass + " ." + self._default.selectMethodList );
		//$( "option", $select ).remove();
		$select.append( "<option value='-1' selected='selected'>-- Select Option --</option>" );
		if( dbKey === -1 )
		{
			return;
		}
		var arr = dbKey.split( "|" );
		var workId = arr[ 0 ];
		var fileName = arr[ 1 ];
		$.each(self._methodList, function( key, method ) {
			self._addValidMethod( $select, workId, fileName, method );
		} );
	},
	
	_addValidMethod : function( $select, workId, fileName, method ) {
		var getFilesByTag = function( fileList ) {
			if( !fileList )
			{
				return;
			}
			$.each( fileList, function( fKey, fName ) {
				if( fName === fileName )
				{
					$select.append( "<option value='" + method + "'>" + method + "</option>" );
					return false;
				}
			} );
		};
		LinkData.getFilesByTag( workId, method, getFilesByTag );
	},
	
	_initUseButtonListener : function() {
		var self = this;
		$( "#" + self._default.baseSequenceContainerId + " ." + self._default.useButtonClass ).click( function() {
			$txtSeq = $( "#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass );
			$fixedSeq = $( "#" + self._default.baseSequenceContainerId + " ." + self._default.fixedSequenceClass );
			self._baseSequence = $txtSeq.val() + $fixedSeq.html();
			$errMsgEl = $( "#" + self._default.baseSequenceContainerId + " ." + self._default.baseErrorMessageClass );
			$errMsgEl.hide();
			if( !self._baseSequence || self._baseSequence.length < self._default.baseSequenceMinLength )
			{
				$errMsgEl.html( self._default.errorMessageEnterSequence.replace( "{0}", self._default.baseSequenceMinLength ) );
				$errMsgEl.show();
				//_showError($baseContainer, opts.msgEmptySequence);
			}
			else
			{
				$txtSeq.attr( "readonly", true ).addClass( "noborder" );
				$( this ).hide();
				$( "." + self._default.appContainerClass ).show();
			}
		} );
	},
	
	_callback : function( self ) {
		$( "." + self._default.appContainerClass + " ." + self._default.nextButtonContainerClass ).show();
		$( "." + self._default.appContainerClass + " ." + self._default.nextButtonClass ).unbind( "click" );
		$( "." + self._default.appContainerClass + " ." + self._default.nextButtonClass ).click( function() {
			$parent = $( this ).closest( "." + self._default.appContainerClass );
			var clone = $parent.clone( true );
			var text = $( clone ).find( ".replaceSequence" ).text();
			if( text && text.trim().length !== 0 ) {
				self._baseSequence = text;
			}
			$( clone ).find( "." + self._default.actionResultContainer ).html( "" );
			$( clone ).find( "." + self._default.nextButtonContainerClass ).hide();
			$parent.parent().append(clone);
		} );
	},
	
	_getDatabaseOptionKey : function( workId, fileName ) {
		return workId + "|" + fileName;
	},
	
	_getLabel : function( value ) {
		var propLabel = value;
		var arr = value.split( "#" );
		if( arr.length > 1 )
		{
			propLabel = decodeURIComponent( arr[ 1 ] );
		}
		return propLabel;
	}
	
};

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

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

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

#gcAppContainer {
	width: 900px;
}

.hidden {
	display:none;
}

.left {
    float: left;
}

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

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

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

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

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

.replaceSequence {
    background-color: #FFFFFF;
    border: 1px solid #DDDDDD;
    margin: 10px 0 0;
	font-family: "Courier New","Lucida Console";
	overflow: auto;
	/*word-wrap: break-word;*/
}

.replace {
    color: #E80010;
}

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

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

.actionButtonContainer {
    text-align: right;
}

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

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

.noborder {
    border: medium none;
}

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

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

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

.databaseInfo .motif {
	width: 70%;
}

/**
 * button css
 */

a.useButton {
	width: 80px;
}

.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 .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;
}

<div id="baseSequenceContainer">
	<div class="label">Base Sequence</div>
	<div class="baseSequenceBox">
		<input type="hidden" class="hdnBaseSequence" value="CGATAAAGGAAAGGCCATCGTTGAAGATGCCTCTGCCGACAGTGGTCCCAAAGATGGACCCCCACCCACGAGGAGCATCGTGGAAAAAGAAGACGTTCCAACCACGTCTTCAAAGCAAGTGGATTGATGTGATAACATGGTGGAGCACGACACACTTGTCTACTCCAAAAATATCAAAGATACAGTCTCAGAAGACCAAAGGGCAATTGAGACTTTTCAACAAAGGGTAATATCCGGAAACCTCCTCGGATTCCATTGCCCAGCTATCTGTCACTTTATTGTGAAGATAGTGGAAAAGGAAGGTGGCTCCTACAAATGCCATCATTGCGATAAAGGAAAGGCCATCGTTGAAGATGCCTCTGCCGACAGTGGTCCCAAAGATGGACCCCCACCCACGAGGAGCATCGTGGAAAAAGAAGACGTTCCAACCACGTCTTCAAAGCAAGTGGATTGATGTGATATCTCCACTGACGTAAGGGATGACGCACAATCCCACTATCGATCCCAAGACCCTTCCTCTATATAAGGAAGTTCATTTCATTTGGAGAGG"/>
		<span>
			<input type="text" class="baseSequence" value=""/></span>
		<span class="fixedSequence"></span>
	</div>
	<div style="margin-top:5px;"><a class="useButton btn btn-green">Use</a></div>
	<div class="baseErrorMessage hidden"></div>
</div>
<div class="applicationContainer hidden">
	<div class="actionButtonContainer">
		<span class="appSummery"></span>
		<span class="collapseButton actionBtn" title="collapse">_</span>
		<span class="expandButton actionBtn" title="expand">+</span>
		<span class="removeButton actionBtn" title="remove">x</span>
		<br clear="all"/>
	</div>
	<div class="applicationDataContainer">
		<div class="row">
			<div class="label left">Select Database</div>
			<div class="left"><select class="databaseList"></select></div>
		</div>
		<div class="row">
			<div class="label left">Sequence App</div>
			<div class="left"><select class="optionList"></select></div>
		</div>
		<div class="actionResultContainer"></div>
		<div class="nextButtonContainer hidden"><a class="btn nextButton">Next</a></div>
	</div>
</div>
</div>

Preview
Input Data
ReadMe
Snapshots

Applications using the same data

Contributor:
Update:
Rating

LinkData Work	Table Data
Circadian Coexpression (DIURNAL + ATTED-II promoter motif) Full Contributor:GenoCon Update:Jan 15, 2013 3424 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,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_COL_SD [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_DD_DDHC [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_LDHC [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_LDHH_SM [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_LDHH_ST [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_LER_SD [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_LIGHT5_HIF138_13 [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_LIGHT5_HIF138_8 [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_LIGHT5_znknOX [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_LL12_LDHH [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_LL23_LDHH [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_LLHC [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_LL_LDHC [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_LL_LLHC [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_lhyox_SD [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_longday [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_lux_2_LDHH [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_phyB9_SD [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_ATTED_shortday [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking]
Circadian Genomic (DIURNAL + PPDB promoter motif) Full Contributor:GenoCon Update:Jan 15, 2013 3282 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,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_COL_SD [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_DD_DDHC [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_LDHC [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_LDHH_SM [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_LDHH_ST [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_LER_SD [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_LIGHT5_HIF138_13 [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_LIGHT5_HIF138_8 [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_LIGHT5_znknOX [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_LL12_LDHH [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_LL23_LDHH [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_LLHC [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_LL_LDHC [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_LL_LLHC [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_lhyox_SD [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_longday [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_lux_2_LDHH [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_phyB9_SD [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking] DiurnalHours_PPDB_shortday [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2,MotifRanking]
Speedup Lists of Circadian Coexpression (DIURNAL + ATTED-II promoter motif) Gene Contributor:GenoCon Update:Jan 15, 2013 985 Downloads, 19 Applications Lists for the Diurnal and ATTED-II mashup data table. For each experiment, the top 1000 and bottom 1000 genes ranked by circadian amplitude. 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 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> label:Expression X hours </th> <td> The genes ranked by absolute expression level after the seedling has been growing for X hours, starting at 7 days. </td> </tr> <tr> <th nowrap> condition:Conditions_Range </th> <td> The genes ranked by absolute expression level under the given condition, and for the given circadian phase range. </td> </tr> </table> <br> <br> --> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s342i/DiurnalHours_ATTED_0to4_top.html#work_information'>DiurnalHours_ATTED_0to4_top</a> </td> <td> Lists for the DIURNAL and ATTED-II mashup data table. For each experiment, the top 1000 genes ranked by absolute expression level, for circadian phase range 0 to 4 hr. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s342i/DiurnalHours_ATTED_4to8_top.html#work_information'>DiurnalHours_ATTED_4to8_top</a> </td> <td> Lists for the DIURNAL and ATTED-II mashup data table. For each experiment, the top 1000 genes ranked by absolute expression level, for circadian phase range 4 to 8 hr. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s342i/DiurnalHours_ATTED_8to12_top.html#work_information'>DiurnalHours_ATTED_8to12_top</a> </td> <td> Lists for the DIURNAL and ATTED-II mashup data table. For each experiment, the top 1000 genes ranked by absolute expression level, for circadian phase range 8 to 12 hr. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s342i/DiurnalHours_ATTED_12to16_top.html#work_information'>DiurnalHours_ATTED_12to16_top</a> </td> <td> Lists for the DIURNAL and ATTED-II mashup data table. For each experiment, the top 1000 genes ranked by absolute expression level, for circadian phase range 12 to 16 hr. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s342i/DiurnalHours_ATTED_16to20_top.html#work_information'>DiurnalHours_ATTED_16to20_top</a> </td> <td> Lists for the DIURNAL and ATTED-II mashup data table. For each experiment, the top 1000 genes ranked by absolute expression level, for circadian phase range 16 to 20 hr. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s342i/DiurnalHours_ATTED_20to24_top.html#work_information'>DiurnalHours_ATTED_20to24_top</a> </td> <td> Lists for the DIURNAL and ATTED-II mashup data table. For each experiment, the top 1000 genes ranked by absolute expression level, for circadian phase range 20 to 24 hr. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s342i/DiurnalHours_ATTED_top.html#work_information'>DiurnalHours_ATTED_top</a> </td> <td> Lists for the DIURNAL and ATTED-II mashup data table. For each experiment, the top 1000 genes ranked by circadian amplitude. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s342i/DiurnalHours_ATTED_bottom.html#work_information'>DiurnalHours_ATTED_bottom</a> </td> <td> Lists for the DIURNAL and ATTED-II mashup data table. For each experiment, the bottom 1000 genes ranked by circadian amplitude. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s342i/DiurnalHours_ATTED_all.html#work_information'>DiurnalHours_ATTED_all</a> </td> <td> Lists for the DIURNAL and ATTED-II mashup data table. For each experiment, the all genes ranked by circadian amplitude. </td> </tr> </table>	DiurnalHours_ATTED_0to4_top [result_top] DiurnalHours_ATTED_12to16_top [result_top] DiurnalHours_ATTED_16to20_top [result_top] DiurnalHours_ATTED_20to24_top [result_top] DiurnalHours_ATTED_4to8_top [result_top] DiurnalHours_ATTED_8to12_top [result_top] DiurnalHours_ATTED_all [] DiurnalHours_ATTED_bottom [result_bottom] DiurnalHours_ATTED_top [result_top]
Developmental Coexpression (AtGenExpress + ATTED-II promoter motif) Full Contributor:GenoCon Update:Mar 6, 2013 2786 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,MotifMaxExpress2,MotifMinExpress2,HighChart2,MotifRanking] AtGenExpress_ATTED_Fruit_Seeds [database,MotifMaxExpress2,MotifMinExpress2,HighChart2,MotifRanking] AtGenExpress_ATTED_Leaf [database,MotifMaxExpress2,MotifMinExpress2,HighChart2,MotifRanking] AtGenExpress_ATTED_Root [database,MotifMaxExpress2,MotifMinExpress2,HighChart2,MotifRanking] AtGenExpress_ATTED_Seedling [database,MotifMaxExpress2,MotifMinExpress2,HighChart2,MotifRanking] AtGenExpress_ATTED_Stem [database,MotifMaxExpress2,MotifMinExpress2,HighChart2,MotifRanking] AtGenExpress_ATTED_Whole_Plant [database,MotifMaxExpress2,MotifMinExpress2,HighChart2,MotifRanking] Heptamer_elements [heptamer] PPDB_position []
Speedup Lists of Developmental Genomic (AtGenExpress + PPDB promoter motif) Gene Contributor:GenoCon Update:Jan 15, 2013 712 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 including MotifRanking Contributor:Masahiro Mochizuki Update:Dec 29, 2012 97 Downloads, 1 Applications 新開発プラグインMotifRankingをを含むプラグイン一覧	Application_Plugins_for_Synthetic_Promoter_Design [method]
Speedup Lists of Developmental Coexpression (AtGenExpress + ATTED-II promoter motif) Gene Contributor:GenoCon Update:Jan 15, 2013 723 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]
Speedup Lists of Circadian Genomic (DIURNAL + PPDB promoter motif) Gene Contributor:GenoCon Update:Jan 15, 2013 1993 Downloads, 23 Applications Lists for the Diurnal and PPDB mashup data table. For each experiment, the top 1000 and bottom 1000 genes ranked by circadian amplitude. 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 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> label:Expression X hours </th> <td> The genes ranked by absolute expression level after the seedling has been growing for X hours, starting at 7 days. </td> </tr> <tr> <th nowrap> condition:Conditions_Range </th> <td> The genes ranked by absolute expression level under the given condition, and for the given circadian phase range. </td> </tr> </table> <br> <br> --> <b> Descriptions for each data table: </b> <table> <tr> <td> <a href='http://linkdata.org/work/rdf1s343i/DiurnalHours_PPDB_0to4_top.html#work_information'>DiurnalHours_PPDB_0to4_top</a> </td> <td> Lists for the DIURNAL and PPDB mashup data table. For each experiment, the top 1000 genes ranked by absolute expression level, for circadian phase range 0 to 4 hr. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s343i/DiurnalHours_PPDB_4to8_top.html#work_information'>DiurnalHours_PPDB_4to8_top</a> </td> <td> Lists for the DIURNAL and PPDB mashup data table. For each experiment, the top 1000 genes ranked by absolute expression level, for circadian phase range 4 to 8 hr. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s343i/DiurnalHours_PPDB_8to12_top.html#work_information'>DiurnalHours_PPDB_8to12_top</a> </td> <td> Lists for the DIURNAL and PPDB mashup data table. For each experiment, the top 1000 genes ranked by absolute expression level, for circadian phase range 8 to 12 hr. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s343i/DiurnalHours_PPDB_12to16_top.html#work_information'>DiurnalHours_PPDB_12to16_top</a> </td> <td> Lists for the DIURNAL and PPDB mashup data table. For each experiment, the top 1000 genes ranked by absolute expression level, for circadian phase range 12 to 16 hr. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s343i/DiurnalHours_PPDB_16to20_top.html#work_information'>DiurnalHours_PPDB_16to20_top</a> </td> <td> Lists for the DIURNAL and PPDB mashup data table. For each experiment, the top 1000 genes ranked by absolute expression level, for circadian phase range 16 to 20 hr. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s343i/DiurnalHours_PPDB_20to24_top.html#work_information'>DiurnalHours_PPDB_20to24_top</a> </td> <td> Lists for the DIURNAL and PPDB mashup data table. For each experiment, the top 1000 genes ranked by absolute expression level, for circadian phase range 20 to 24 hr. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s343i/DiurnalHours_PPDB_top.html#work_information'>DiurnalHours_PPDB_top</a> </td> <td> Lists for the DIURNAL 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/rdf1s343i/DiurnalHours_PPDB_bottom.html#work_information'>DiurnalHours_PPDB_bottom</a> </td> <td> Lists for the DIURNAL and PPDB (Plant Promoter Database) mashup data table. For each experiment, the bottom 1000 genes ranked by circadian amplitude. </td> </tr> <tr> <td> <a href='http://linkdata.org/work/rdf1s343i/DiurnalHours_PPDB_all.html#work_information'>DiurnalHours_PPDB_all</a> </td> <td> Lists for the DIURNAL and PPDB (Plant Promoter Database) mashup data table. For each experiment, the all genes ranked by circadian amplitude. </td> </tr> </table>	DiurnalHours_PPDB_0to4_top [result_top] DiurnalHours_PPDB_12to16_top [result_top] DiurnalHours_PPDB_16to20_top [result_top] DiurnalHours_PPDB_20to24_top [result_top] DiurnalHours_PPDB_4to8_top [result_top] DiurnalHours_PPDB_8to12_top [result_top] DiurnalHours_PPDB_all [] DiurnalHours_PPDB_bottom [result_bottom] DiurnalHours_PPDB_top [result_top]
Developmental Genomic (AtGenExpress + PPDB promoter motif) Full Contributor:GenoCon Update:Jan 22, 2013 1670 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,MotifMaxExpress2,MotifMinExpress2,HighChart2,MotifRanking] AtGenExpress_PPDB_Fruit_Seeds [database,MotifMaxExpress2,MotifMinExpress2,HighChart2,MotifRanking] AtGenExpress_PPDB_Leaf [database,MotifMaxExpress2,MotifMinExpress2,HighChart2,MotifRanking] AtGenExpress_PPDB_Root [database,MotifMaxExpress2,MotifMinExpress2,HighChart2,MotifRanking] AtGenExpress_PPDB_Seedling [database,MotifMaxExpress2,MotifMinExpress2,HighChart2,MotifRanking] AtGenExpress_PPDB_Stem [database,MotifMaxExpress2,MotifMinExpress2,HighChart2,MotifRanking] AtGenExpress_PPDB_Whole_Plant [database,MotifMaxExpress2,MotifMinExpress2,HighChart2,MotifRanking] Octamer_elements [octamer]

Link http://app.linkdata.org/run/app1s137i?tab=readme

<div style="display: block;" id="readMeCodeEditorContainer" class="editorTab">
								<div id="readmeContent"><div id="swf_body">
<div id="wiki">
<h1>新開発プラグインMotifRankingによる、稔性を考慮したプロモーター設計 <br></h1><div align="right"><blockquote><p>望月 正弘<br></p></blockquote></div><hr>

<h2>1. プロモーター設計の概要</h2><blockquote><p>本デザインでは、LinkData.org上のCADプログラムを用い、以下の手順でプロモーターを作製した。<br></p>
<ol>
<li>デザインの基礎となる天然のプロモーター配列には、デフォルトの35Sカリフラワーモザイクウイルス由来のプロモーターを採用した。</li>
<li>データベースとしてAtGenExpress_ATTED_Root、アプリケーションとして今回開発したプラグインMotifRankingを用い、プロパティCol-0_root_GM-21で発現量を示すスコアが4番目に高い遺伝子座<a target="_blank" href="http://www.arabidopsis.org/servlets/TairObject?type=locus&name=At3g15950">At3g15950</a>のモチーフを1の配列に組込んだ。</li>
<li>データベースとしてAtGenExpress_ATTED_Flowering、アプリケーションとしてMotifRankingを用い、プロパティCol-0_pollenでスコアが7番目に低い遺伝子座<a target="_blank" href="http://www.arabidopsis.org/servlets/TairObject?type=locus&name=At4g23670">At4g23670</a>のモチーフを2の配列に組込んだ。</li></ol><p>
<br></p></blockquote><h2>2. デザインと新開発プラグインの狙い<br></h2><h3>2-1. 組織特異的プロモーターによる稔性維持</h3><blockquote><p>　本デザインは、組換え後の稔性を維持することが遺伝子組換え植物の作製において重要であることを指摘し、その方法として組織特異的プロモーターの利用を提案するものである。</p><p>　私は、GenoConに取り組む過程で、哺乳類のシトクロムP-450 2E1の遺伝子を植物に導入することでホルムアルデヒド耐性を付与できるとするZhengらの研究[1]を知った。同時に、この結果はChallenge Bの課題に合致するものの、そのままGenoConに転用するには一つの懸念事項が存在することにも気づいた。それは、Zhengらのペチュニア<i>Petunia hybrida</i>を用いた実験では形質転換体が種子形成能を欠いていたという点である。Zhengらはリーフディスク法により無性的に形質転換体を得たのに対し、GenoCon 2010では形質転換後に種子を採取しT2世代を実験審査に用いていた[2, 3]。従って、Zhengらと同じ方法を採用しても、形質転換後に種子が得られなければ、GenoConでは実験そのものが成立しないおそれがある。この例に限らず、一般論としても遺伝子導入に伴う不稔は、遺伝子組換え植物の作製とその継続的栽培を困難にし、特に商品作物の場合には種子や果実の形成不全自体が商品価値を大きく毀損する可能性がある。</p><p>　この課題を克服するための一案として、組織特異的プロモーターの作成を試みた。この人工プロモーターは、土壌のファイトレメディエーションへの応用を想定して、根で目的遺伝子を高発現し、逆に生殖に直接関与する花粉においてその発現を抑制するように設計されている。この発現制御によって、外来遺伝子による花粉への悪影響を限定し、遺伝子導入に伴う不稔化が防止されるものと期待される。</p><p>　なお、本デザインは不稔の原因が花粉での目的遺伝子発現にある場合に限り有効なものであり、実際には不稔の原因に応じて適切な組織において発現を抑制することが求められる。 <br></p></blockquote>

<h3>2-2. 新開発プラグインMotifRankingはプロモーター設計の自由度を拡大する</h3><blockquote>
<a target="_blank" href="http://app.linkdata.org/asset/7fde2015.png">
<img src="http://app.linkdata.org/asset/7fde2015.png" title="図1" alt="新開発プラグインの優位性" style="width: 70%;">
</a>
<br>
<br>　GenoCon Challenge Aの公式CADプログラムには、元々MotifMax2、MotifMin2というプラグインが用意されている。これらのプラグインは、設定された条件下でそれぞれ最大/最小の発現を誘導すると予測される遺伝子座のモチーフを自動的に選び出し、これをプロモータ配列に組み込む機能を有している (図1:A)。一方、新開発プラグインMotifRankingは、上位/下位10件の発現量ランキングを表示し、ユーザーがそこから任意の遺伝子座を選べるように拡張されている (図1:B)。このプラグインには、既存のプラグインに比べて、以下のような利点がある。<br><ol><li>MotifMax2、MotifMin2の場合には、最大・最小の発現量を誘導するモチーフがGenoCon Challenge Aでデザイン可能な範囲に収まらず、警告が表示されることがある。MotifRankingなら上位・下位ランキングの2位以下の遺伝子座から、範囲に収まる別のモチーフを選び出すことができる。</li><li>一つのプロモーターに多重的にモチーフを組込んだ場合には、あるモチーフAが別のモチーフBで上書きされてしまうことがある。MotifRankingを使えば、ランキングの中から相互に衝突しないモチーフの組み合わせを探す余地がある。</li><li>敢えて緩やかな発現制御を行いたい場合には、ランキングで中位のモチーフを選ぶことで、それを実現できる可能性がある。</li></ol>　実際、本デザインでは、上記1の理由から、根での高発現を誘導するモチーフをランキングの上位から順番にチェックし、警告が表示されない4位の遺伝子座を選択した。さらに、上記1と2の理由から、花粉での低発現を実現するモチーフのうち1位から6位のものは避けて、7位のモチーフを採用した。<br></blockquote><br><h2>3. 参考文献</h2>
<ol>
<li><span>D. Zhang, T. Xiang, P. Li, L. Bao, <i>Genetics and molecular biology </i> <b>
  34</b>, 634 (2011).</span> <a target="_blank" href="http://view.ncbi.nlm.nih.gov/pubmed/22215968">[Pubmed]</a></li>
<li>GenoCon 2010審査結果 <a href="https://database.riken.jp/sw/ja/%E5%AE%9F%E9%A8%93%E5%AF%A9%E6%9F%BB%E7%B5%90%E6%9E%9C/cria303s2ria303s1i/">[link]</a></li>
</ol>
</div>
</div>
</div>
</div>