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if (typeof Application == "undefined" || !Application) { var Application = {}; } Application.genocon = function() { this._init.apply(this, arguments); }; Application.genocon.prototype = { _baseSequence : 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", methodFilteringProperty : "#application%20URL", baseSequenceMinLength : 50 }, _init : function() { this._initBaseInput(); 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); }); }, _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>"); $.each(LinkData.getFiles(), function(workId, fileNameList) { $.each(fileNameList, function(key, fileName) { var dbKey = self._getDatabaseOptionKey(workId, fileName); $.each(LinkData.getProperties(workId, fileName), function(pKey, pValue) { if (pValue.indexOf(self._default.databaseFilteringProperty) > 0) { $select.append("<option value='" + dbKey + "'>" + fileName + "</option>"); } }); }); }); }, _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>"); $.each(LinkData.getFiles(), function(workId, fileNameList) { $.each(fileNameList, function(key, fileName) { $.each(LinkData.getProperties(workId, fileName), function(pKey, pValue) { if (pValue.indexOf(self._default.methodFilteringProperty) > 0) { $.each(LinkData.getTriplesByProperty(workId, fileName, pValue), function(tKey, tValue) { var label = self._getLabel(tValue.subject); $select.append("<option value='" + tValue.object + "'>" + label + "</option>"); }); } }); }); }); }, _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.selectMethodList + " option").removeAttr("selected"); $(parent).find("." + self._default.nextButtonContainerClass).hide(); $container = $(parent).find("." + self._default.actionResultContainer); $container.html(""); }); }, _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); $container = $(parent).find("." + self._default.actionResultContainer); $container.html(""); $(parent).find("." + self._default.nextButtonContainerClass).hide(); var date = new Date(); var id = "container_id_" + date.getTime(); $container.attr("id", id); var method = $("option:selected", $(this)).text(); var database = $("option:selected", $(parent).find("." + self._default.selectDataBaseList)).val(); var func = function() { self._callback(self); } if (database != -1) { var arr = database.split("|"); var obj = { workId : arr[0], fileName : arr[1], appName : method, baseSequence : self._baseSequence, callback : func }; eval(method)(id, obj); } }); }, _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() { 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; } /** * 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; }
<div id="gcAppContainer"> <div id="baseSequenceContainer"> <div class="label">Base Sequence</div> <div class="baseSequenceBox"> <input type="hidden" class="hdnBaseSequence" value="GTCAACATGGTGGAGCACGACACTCTCGTCTACTCCAAGAATATCAAAGATACAGTCTCAGAAGACCAGAGGGCTATTGAGACTTTTCAACAAAGTTAATGCGAGGGAAACCTCCTCGGATTCCATTGCCCAGCTATCTGTCACTTCATCGAAAGGACAAGTGAAAGAGAAGATGGCTTCTACAAATGCCATCATTGCGATAAAGGAAAGGCTATCGTTCAAGATGCCTCTACCGACAGTGGTCCCAAAGATGGACCCCCACCCACGAGGAACATCTAGGGGAAAAAAGACGTTCCAACCACGTCTTCAAAGCAAGTGATTGGATTAAGGTTCTTCCACACGGTAAGGGATGGCACTAACACCTACCATCCTTCGCAAGACCCTTCCTCTATATAAGGAAGTTCATTTCATTTGGAGAGGACCTCGAC"/> <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>
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Snapshots
LinkData Work
Table Data
GenoCon2 Challenge A - Developmental conditions
Contributor:GenoCon
Update:Sep 11, 2012
5715 Downloads, 16 Applications
Flowering
Fruit_Seeds
Leaf
Root
Seedling
Stem
Whole_Plant
GenoCon2 Challenge A - Developmental Coexpression (AtGenExpress + ATTED-II promoter motif)
Contributor:GenoCon
Update:Jan 17, 2013
4431 Downloads, 12 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 tissues, with one category for seedlings (8 days old or less) and another for whole plants (older than 8 days). <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>
AtGenExpress_ATTED_Flowering
AtGenExpress_ATTED_Fruit_Seeds
AtGenExpress_ATTED_Leaf
AtGenExpress_ATTED_Root
AtGenExpress_ATTED_Seedling
AtGenExpress_ATTED_Stem
AtGenExpress_ATTED_Whole_Plant
Heptamer_elements
GenoCon2 Challenge A - Circadian Coexpression (DIURNAL + ATTED-II promoter motif)
Contributor:GenoCon
Update:Sep 19, 2012
8505 Downloads, 10 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. <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>
DiurnalHours_ATTED_COL_LDHH
DiurnalHours_ATTED_COL_SD
DiurnalHours_ATTED_DD_DDHC
DiurnalHours_ATTED_LDHC
DiurnalHours_ATTED_LDHH_SM
DiurnalHours_ATTED_LDHH_ST
DiurnalHours_ATTED_LER_SD
DiurnalHours_ATTED_LIGHT5_HIF138_13
DiurnalHours_ATTED_LIGHT5_HIF138_8
DiurnalHours_ATTED_LIGHT5_znknOX
DiurnalHours_ATTED_LL12_LDHH
DiurnalHours_ATTED_LL23_LDHH
DiurnalHours_ATTED_LLHC
DiurnalHours_ATTED_LL_LDHC
DiurnalHours_ATTED_LL_LLHC
DiurnalHours_ATTED_lhyox_SD
DiurnalHours_ATTED_longday
DiurnalHours_ATTED_lux_2_LDHH
DiurnalHours_ATTED_phyB9_SD
DiurnalHours_ATTED_shortday
GenoCon2 Challenge A - Diurnal conditions
Contributor:GenoCon
Update:Sep 19, 2012
1153 Downloads, 8 Applications
Circadian_condition
Diurnal_condition
GenoCon2 Challenge A - Sequence Function Plugins
Contributor:GenoCon
Update:Oct 16, 2012
1488 Downloads, 12 Applications
Application_Plugins_for_Synthetic_Promoter_Design
[
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GenoCon2 Challenge A - Circadian Genomic (DIURNAL + PPDB promoter motif)
Contributor:GenoCon
Update:Sep 21, 2012
8908 Downloads, 8 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.. <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>
DiurnalHours_PPDB_COL_LDHH
DiurnalHours_PPDB_COL_SD
DiurnalHours_PPDB_DD_DDHC
DiurnalHours_PPDB_LDHC
DiurnalHours_PPDB_LDHH_SM
DiurnalHours_PPDB_LDHH_ST
DiurnalHours_PPDB_LER_SD
DiurnalHours_PPDB_LIGHT5_HIF138_13
DiurnalHours_PPDB_LIGHT5_HIF138_8
DiurnalHours_PPDB_LIGHT5_znknOX
DiurnalHours_PPDB_LL12_LDHH
DiurnalHours_PPDB_LL23_LDHH
DiurnalHours_PPDB_LLHC
DiurnalHours_PPDB_LL_LDHC
DiurnalHours_PPDB_LL_LLHC
DiurnalHours_PPDB_lhyox_SD
DiurnalHours_PPDB_longday
DiurnalHours_PPDB_lux_2_LDHH
DiurnalHours_PPDB_phyB9_SD
DiurnalHours_PPDB_shortday
GenoCon2 Challenge A - Developmental Genomic (AtGenExpress + PPDB promoter motif)
Contributor:GenoCon
Update:Sep 21, 2012
3203 Downloads, 8 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 tissues, 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). <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>
AtGenExpress_PPDB_Flowering
AtGenExpress_PPDB_Fruit_Seeds
AtGenExpress_PPDB_Leaf
AtGenExpress_PPDB_Root
AtGenExpress_PPDB_Seedling
AtGenExpress_PPDB_Stem
AtGenExpress_PPDB_Whole_Plant
Octamer_elements
Add LinkData work(LinkData)
Link http://app.linkdata.org/run/app1s77i?tab=readme
Initial content
jquery-1.7.1.min.js
HighChart
jquery-ui-1.8.18.min.js
http://code.highcharts.com/highcharts.js
http://code.highcharts.com/modules/exporting.js
MotifMinExpress
MotifMaxExpress
MotifMaxCircadian
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