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ints_demo.html
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<!-- : /share/cvs/org/yeastgenome/templates/Reports/LocusReport/InteractionServer/result.tmpl,v --> <!-- : /share/cvs/org/yeastgenome/templates/Reports/LocusReport/page_header.tmpl,v --> <!-- : /share/cvs/org/yeastgenome/templates/doc_head.tmpl,v --> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
<title> Interaction Server</title> <!-- : /share/cvs/org/yeastgenome/templates/Reports/LocusReport/InteractionServer/Attic/site_css.tmpl,v -->
<link href="http://yeastgenome-hitz-dev.stanford.edu/css/Site.css" rel="stylesheet" type="text/css" ./>
<link href="http://yeastgenome-hitz-dev.stanford.edu/css/InteractionServer.css" rel="stylesheet" type="text/css" />
<link href="/INT/css/sunny/jquery-ui-1.8.13.custom.css" rel="stylesheet" type="text/css" />
<link href="http://yeastgenome-hitz-dev.stanford.edu/css/jquery-layout-default.css" rel="stylesheet" type="text/css" />
<link href="http://yeastgenome-hitz-dev.stanford.edu/css/farbtastic.css" rel="stylesheet" type="text/css" />
<style type="text/css">
/* give outer-panes their own colors */
.ui-layout-center { background: #CEE; }
.ui-layout-west { background: #CCF; }
.property input.colour_sample_bg {
background-image:url("/INT/images/input_for_colour_picker/bg.png");
background-position:right center;
background-repeat:repeat-y;
}
input, button, textarea, select {
-moz-border-radius:4px 4px 4px 4px;
border:1px solid #C1C1C1;
font-family:Helvetica,Arial,Verdana,sans-serif;
font-size:100%;
padding:0.25em;
}
.floating_widget {
-moz-border-radius:4px 4px 4px 4px;
-moz-box-shadow:0 0 50px #BBBBBB;
background:none repeat scroll 0 0 rgba(54, 54, 54, 0.8);
z-index:9999;
}
#colour_picker {
clear:both;
height:200px;
width:200px;
}
#colour_picker .header {
left:0;
position:absolute;
top:0;
z-index:1;
}
.farbtastic .wheel {
background:url("/INT/images/farbtastic/wheel.png") no-repeat scroll 0 0 transparent;
height:195px;
width:195px;
}
.farbtastic .overlay {
background:url("/INT/images/farbtastic/mask.png") no-repeat scroll 0 0 transparent;
}
.farbtastic .marker {
background:url("/INT/images/farbtastic/marker.png") no-repeat scroll 0 0 transparent;
height:17px;
margin:-8px 0 0 -8px;
overflow:hidden;
width:17px;
}
#nodes input {
display: inline;
float: left;
}
#nodes label.style {
font-size: 12px;
clear:both;
display:block;
}
#nodes label.style_head {
font-size: 12px;
font-weight: bold;
clear:both;
display:block;
}
#color_all_nodes {
border:2px solid #C1C1C1;
}
.ui-validation-error {
background:none repeat scroll 0 0 #FFECEC !important;
border-color:#FF0000 !important;
}
.ui-validation-error:focus {
-moz-box-shadow:0 0 5px #FF0000 !important;
}
.ui-validation-error-message {
color:#FF0000;
}
</style> <!-- put page specific css files here or else in <style> @import -->
<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1" >
</head>
<body>
<div id="wrapper"> <!-- : /share/cvs/org/yeastgenome/templates/header.tmpl,v --> <div id="header_top">
<hr>
<div class="float" id="logo"><a href="http://yeastgenome-hitz-dev.stanford.edu/"><img alt="SGD" src="http://yeastgenome-hitz-dev.stanford.edu/images/SGD_logo.gif" ></a> </div>
<div class="float inline" id="quicksearch">
<ul>
<li><form method="get" action="http://yeastgenome-hitz-dev.stanford.edu/cgi-bin/search/quickSearch.fpl">
<p><input type="text" name="query" size="13" ></p>
<p><input type="submit" name="Submit" value="Search" ></p>
</form></li>
</ul>
</div>
<div class="float inline" id="nav_aid">
<ul>
<li><a href="http://yeastgenome-hitz-dev.stanford.edu/sitemap.html">Site Map</a> | </li>
<li><a href="http://yeastgenome-hitz-dev.stanford.edu/SearchContents.shtml">Search Options</a> | </li>
<li><a href="http://yeastgenome-hitz-dev.stanford.edu/HelpContents.shtml">Help</a> | </li>
<li><a href="http://yeastgenome-hitz-dev.stanford.edu/">Home</a> | </li>
<li><a title="Contact SGD" onMouseover="showtip(this,event,'Contact SGD')" onMouseout="hidetip()" href="http://yeastgenome-hitz-dev.stanford.edu/cgi-bin/suggestion"><img alt='Contact SGD' class='bottom' src="http://yeastgenome-hitz-dev.stanford.edu/images/mail.gif"> </a> | </li>
<li><a type="application/rss+xml" href="http://yeastgenome-hitz-dev.stanford.edu/xml/news_feed.xml"><img alt='RSS' class='bottom' src="http://yeastgenome-hitz-dev.stanford.edu/images/rss.gif"> </a> </li>
</ul>
</div><!-- end of navigation aid -->
<div class="inline" id="tool_bar">
<ul>
<li> <!-- spacer kludge --> </li>
<li><a href="http://yeastgenome-hitz-dev.stanford.edu/ComContents.shtml">Community Info</a></li>
<li><a href="http://yeastgenome-hitz-dev.stanford.edu/SubmitContents.shtml">Submit Data</a></li>
<li><a href="http://yeastgenome-hitz-dev.stanford.edu/cgi-bin/blast-sgd.pl">BLAST</a></li>
<li><a href="http://yeastgenome-hitz-dev.stanford.edu/cgi-bin/web-primer">Primers</a></li>
<li><a href="http://yeastgenome-hitz-dev.stanford.edu/cgi-bin/PATMATCH/nph-patmatch">PatMatch</a></li>
<li><a href="http://yeastgenome-hitz-dev.stanford.edu/cgi-bin/seqTools">Gene/Seq Resources</a></li>
<li><a href="http://yeastgenome-hitz-dev.stanford.edu/cgi-bin/search/featureSearch">Advanced Search</a></li>
<li><a href="http://yeastgenome-devwiki.stanford.edu/">Community Wiki</a></li>
</ul>
</div><!-- end of tool bar -->
<div class="spacer"></div>
<hr>
</div> <!-- end of header -->
<div id="main_page"> <div class="spacer" id='center_title'>
<h2 class="inline">
<span class="gene_name"></span> Interaction Server <a class="help" name="top" href='http://yeastgenome-hitz-dev.stanford.edu/help/PhysGenIntDetailsHelp.html'><img alt="Help" src='http://yeastgenome-hitz-dev.stanford.edu/images/help-button.gif'></a> </h2> </div>
<!-- page header includes content div -->
<div id="viewer">
<div id="cytoscapeweb_container" class="ui-layout-center">
<div id="cytoscapeweb">
Cytoscape Web will replace the contents of this div with your graph.
<embed id="CytoscapeWeb1" width="100%" height="100%" align="middle" type="application/x-shockwave-flash" flashvars="id=CytoscapeWeb1" wmode="opaque" pluginspage="http://www.adobe.com/go/getflashplayer" allowscriptaccess="always" name="cytoscapeweb" bgcolor="#CCCCFF" quality="high" src="/INT/swf/CytoscapeWeb.swf">
</div>
</div>
<div id="panel" class="ui-layout-west">
<div id="west-north">
<h3><a href="#">Gene Info</a></h3>
<div id='search_box' class='ui-widget'>
<label for="search">Enter Gene: </label>
<input id="search" size=6>
</div>
<div id="gene_info_tabs" style="font-size: 16px;">
<ul>
<li><a href="#info_basic">Basic Info</a></li>
<li><a href="#info_go">GO</a></li>
<li><a href="#info_pheno">Phenotype</a></li>
</ul>
<div id="info_basic"><p>Click on a Gene node to display</p></div>
<div id="info_go"><p>Click on a Gene node to display</p></div>
<div id="info_pheno"><p>Click on a Gene node to display</p></div>
</div>
</div>
<div id="west-center">
<h3><a href="#">Legend</a></h3> <!-- : /share/cvs/org/yeastgenome/templates/Reports/LocusReport/InteractionServer/legend.tmpl,v -->
<div id="legend">
<div id="nodes">
<h2>Term Name / GO ID</h2>
<div id="reset">
<input id="networkReset" type="reset" name="networkResetButton" value="Reset Network" >
</div>
<div id="get">
<input id="getNetwork" type="text" size=6>
</div>
<div class="property" type="colour" property="ALL">
<label class="style_head" for="color_all_nodes">Color all nodes</label>
<input id="color_all_nodes" type="text" name="ALL_nodes" value="#CCCCCC">
</div>
</div>
<div id="node_color"> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0009405">
<label class="style" for="GO:0009405_color"> <span class="b i">(0)</span> pathogenesis (GO:0009405)</label>
<input id="pathogenesis" type="text" name="pathogenesis" value="#CCCCCC" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0008219">
<label class="style" for="GO:0008219_color"> <span class="b i">(0)</span> cell death (GO:0008219)</label>
<input id="cell_death" type="text" name="cell death" value="#999999" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0050789">
<label class="style" for="GO:0050789_color"> <span class="b i">(0)</span> regulation of biological process (GO:0050789)</label>
<input id="regulation_of_biological_process" type="text" name="regulation of biological process" value="#FFFFFF" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0009653">
<label class="style" for="GO:0009653_color"> <span class="b i">(7)</span> anatomical structure morphogenesis (GO:0009653)</label>
<input id="anatomical_structure_morphogenesis" type="text" name="anatomical structure morphogenesis" value="#00CC66" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006996">
<label class="style" for="GO:0006996_color"> <span class="b i">(3)</span> organelle organization and biogenesis (GO:0006996)</label>
<input id="organelle_organization_and_biogenesis" type="text" name="organelle organization and biogenesis" value="#00CC99" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0042254">
<label class="style" for="GO:0042254_color"> <span class="b i">(1)</span> ribosome biogenesis and assembly (GO:0042254)</label>
<input id="ribosome_biogenesis_and_assembly" type="text" name="ribosome biogenesis and assembly" value="#00FF00" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0007047">
<label class="style" for="GO:0007047_color"> <span class="b i">(2)</span> cell wall organization and biogenesis (GO:0007047)</label>
<input id="cell_wall_organization_and_biogenesis" type="text" name="cell wall organization and biogenesis" value="#00CC66" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0007010">
<label class="style" for="GO:0007010_color"> <span class="b i">(3)</span> cytoskeleton organization and biogenesis (GO:0007010)</label>
<input id="cytoskeleton_organization_and_biogenesis" type="text" name="cytoskeleton organization and biogenesis" value="#33FF99" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006412">
<label class="style" for="GO:0006412_color"> <span class="b i">(1)</span> translation (GO:0006412)</label>
<input id="translation" type="text" name="translation" value="#CCFF99" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0043062">
<label class="style" for="GO:0043062_color"> <span class="b i">(0)</span> extracellular structure organization and biogenesis (GO:0043062)</label>
<input id="extracellular_structure_organization_and_biogenesis" type="text" name="extracellular structure organization and biogenesis" value="#00CC99" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006997">
<label class="style" for="GO:0006997_color"> <span class="b i">(1)</span> nuclear organization and biogenesis (GO:0006997)</label>
<input id="nuclear_organization_and_biogenesis" type="text" name="nuclear organization and biogenesis" value="#66FF99" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0016044">
<label class="style" for="GO:0016044_color"> <span class="b i">(2)</span> membrane organization and biogenesis (GO:0016044)</label>
<input id="membrane_organization_and_biogenesis" type="text" name="membrane organization and biogenesis" value="#339966" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0007126">
<label class="style" for="GO:0007126_color"> <span class="b i">(0)</span> meiosis (GO:0007126)</label>
<input id="meiosis" type="text" name="meiosis" value="#CC66FF" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0007114">
<label class="style" for="GO:0007114_color"> <span class="b i">(2)</span> cell budding (GO:0007114)</label>
<input id="cell_budding" type="text" name="cell budding" value="#9933FF" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0007049">
<label class="style" for="GO:0007049_color"> <span class="b i">(5)</span> cell cycle (GO:0007049)</label>
<input id="cell_cycle" type="text" name="cell cycle" value="#9966FF" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0000746">
<label class="style" for="GO:0000746_color"> <span class="b i">(10)</span> conjugation (GO:0000746)</label>
<input id="conjugation" type="text" name="conjugation" value="#9933CC" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0000910">
<label class="style" for="GO:0000910_color"> <span class="b i">(2)</span> cytokinesis (GO:0000910)</label>
<input id="cytokinesis" type="text" name="cytokinesis" value="#9900CC" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006944">
<label class="style" for="GO:0006944_color"> <span class="b i">(0)</span> membrane fusion (GO:0006944)</label>
<input id="membrane_fusion" type="text" name="membrane fusion" value="#CC9966" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0030154">
<label class="style" for="GO:0030154_color"> <span class="b i">(0)</span> cell differentiation (GO:0030154)</label>
<input id="cell_differentiation" type="text" name="cell differentiation" value="#993300" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0030435">
<label class="style" for="GO:0030435_color"> <span class="b i">(1)</span> sporulation (GO:0030435)</label>
<input id="sporulation" type="text" name="sporulation" value="#663333" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0016192">
<label class="style" for="GO:0016192_color"> <span class="b i">(2)</span> vesicle-mediated transport (GO:0016192)</label>
<input id="vesicle-mediated_transport" type="text" name="vesicle-mediated transport" value="#996633" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0019725">
<label class="style" for="GO:0019725_color"> <span class="b i">(1)</span> cell homeostasis (GO:0019725)</label>
<input id="cell_homeostasis" type="text" name="cell homeostasis" value="#996600" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0046903">
<label class="style" for="GO:0046903_color"> <span class="b i">(0)</span> secretion (GO:0046903)</label>
<input id="secretion" type="text" name="secretion" value="#663300" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0007124">
<label class="style" for="GO:0007124_color"> <span class="b i">(2)</span> pseudohyphal growth (GO:0007124)</label>
<input id="pseudohyphal_growth" type="text" name="pseudohyphal growth" value="#996666" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006928">
<label class="style" for="GO:0006928_color"> <span class="b i">(0)</span> cell motility (GO:0006928)</label>
<input id="cell_motility" type="text" name="cell motility" value="#CC9900" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0007165">
<label class="style" for="GO:0007165_color"> <span class="b i">(14)</span> signal transduction (GO:0007165)</label>
<input id="signal_transduction" type="text" name="signal transduction" value="#FF9933" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006350">
<label class="style" for="GO:0006350_color"> <span class="b i">(2)</span> transcription (GO:0006350)</label>
<input id="transcription" type="text" name="transcription" value="#FFFF00" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0007610">
<label class="style" for="GO:0007610_color"> <span class="b i">(0)</span> behavior (GO:0007610)</label>
<input id="behavior" type="text" name="behavior" value="#CC3300" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006950">
<label class="style" for="GO:0006950_color"> <span class="b i">(3)</span> response to stress (GO:0006950)</label>
<input id="response_to_stress" type="text" name="response to stress" value="#FF6633" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006464">
<label class="style" for="GO:0006464_color"> <span class="b i">(3)</span> protein modification (GO:0006464)</label>
<input id="protein_modification" type="text" name="protein modification" value="#FF5050" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0007154">
<label class="style" for="GO:0007154_color"> <span class="b i">(0)</span> cell communication (GO:0007154)</label>
<input id="cell_communication" type="text" name="cell communication" value="#FFCC99" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0016070">
<label class="style" for="GO:0016070_color"> <span class="b i">(4)</span> RNA metabolic process (GO:0016070)</label>
<input id="RNA_metabolic_process" type="text" name="RNA metabolic process" value="#0000FF" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0005975">
<label class="style" for="GO:0005975_color"> <span class="b i">(2)</span> carbohydrate metabolic process (GO:0005975)</label>
<input id="carbohydrate_metabolic_process" type="text" name="carbohydrate metabolic process" value="#3399CC" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006629">
<label class="style" for="GO:0006629_color"> <span class="b i">(0)</span> lipid metabolic process (GO:0006629)</label>
<input id="lipid_metabolic_process" type="text" name="lipid metabolic process" value="#0066FF" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0043170">
<label class="style" for="GO:0043170_color"> <span class="b i">(0)</span> macromolecule metabolic process (GO:0043170)</label>
<input id="macromolecule_metabolic_process" type="text" name="macromolecule metabolic process" value="#000066" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006139">
<label class="style" for="GO:0006139_color"> <span class="b i">(0)</span> nucleobase, nucleoside, nucleotide and nucleic acid metabolic process (GO:0006139)</label>
<input id="nucleobase_nucleoside_nucleotide_and_nucleic_acid_metabolic_process " type="text" name="nucleobase, nucleoside, nucleotide and nucleic acid metabolic process " value="#00CCFF" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006519">
<label class="style" for="GO:0006519_color"> <span class="b i">(2)</span> amino acid and derivative metabolic process (GO:0006519)</label>
<input id="amino_acid_and_derivative_metabolic_process" type="text" name="amino acid and derivative metabolic process" value="#99CCFF" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006766">
<label class="style" for="GO:0006766_color"> <span class="b i">(0)</span> vitamin metabolic process (GO:0006766)</label>
<input id="vitamin_metabolic_process" type="text" name="vitamin metabolic process" value="#0000CC" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006259">
<label class="style" for="GO:0006259_color"> <span class="b i">(0)</span> DNA metabolic process (GO:0006259)</label>
<input id="DNA_metabolic_process" type="text" name="DNA metabolic process" value="#0033FF" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006810">
<label class="style" for="GO:0006810_color"> <span class="b i">(4)</span> transport (GO:0006810)</label>
<input id="transport" type="text" name="transport" value="#FF3333" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006091">
<label class="style" for="GO:0006091_color"> <span class="b i">(1)</span> generation of precursor metabolites and energy (GO:0006091)</label>
<input id="generation_of_precursor_metabolites_and_energy" type="text" name="generation of precursor metabolites and energy" value="#FF33CC" >
</div> <div class="property" type="colour" property="GO_SLIM.PROCESS.GO:0006118">
<label class="style" for="GO:0006118_color"> <span class="b i">(0)</span> electron transport (GO:0006118)</label>
<input id="electron_transport" type="text" name="electron transport" value="#FF66CC" >
</div> </div>
</div>
<table id ="node_shape_legend" class="plain_subtable" style="max-width: 300px;">
<thead>
<tr>
<th class="alt_table_header" colspan="4">Node Shapes</th>
</tr><tr>
<th class="table_header">Term Name / GO ID</th>
<th class="table_header" colspan="2">Shape</th>
</tr>
<tbody> <tr style="border: 1;">
<td>translation regulator activity</td> <td rowspan="4">parallelogram</td> </tr><tr>
<td>GO:0045182</td>
</tr> <tr style="border: 1;">
<td>transcription regulator activity</td> </tr><tr>
<td>GO:0030528</td>
</tr> <tr style="border: 1;">
<td>carrier activity</td> <td rowspan="26">ellipse</td> </tr><tr>
<td>GO:0005386</td>
</tr> <tr style="border: 1;">
<td>electron carrier activity</td> </tr><tr>
<td>GO:0009055</td>
</tr> <tr style="border: 1;">
<td>transporter activity</td> </tr><tr>
<td>GO:0005215</td>
</tr> <tr style="border: 1;">
<td>ion transporter activity</td> </tr><tr>
<td>GO:0015075</td>
</tr> <tr style="border: 1;">
<td>binding</td> </tr><tr>
<td>GO:0005488</td>
</tr> <tr style="border: 1;">
<td>channel or pore class transporter activity</td> </tr><tr>
<td>GO:0015267</td>
</tr> <tr style="border: 1;">
<td>permease activity</td> </tr><tr>
<td>GO:0015646</td>
</tr> <tr style="border: 1;">
<td>protein transporter activity</td> </tr><tr>
<td>GO:0008565</td>
</tr> <tr style="border: 1;">
<td>protein binding</td> </tr><tr>
<td>GO:0005515</td>
</tr> <tr style="border: 1;">
<td>integrase activity</td> </tr><tr>
<td>GO:0008907</td>
</tr> <tr style="border: 1;">
<td>structural molecule activity</td> </tr><tr>
<td>GO:0005198</td>
</tr> <tr style="border: 1;">
<td>receptor activity</td> </tr><tr>
<td>GO:0004872</td>
</tr> <tr style="border: 1;">
<td>antioxidant activity</td> </tr><tr>
<td>GO:0016209</td>
</tr> <tr style="border: 1;">
<td>signal transducer activity</td> <td rowspan="2">triangle</td> </tr><tr>
<td>GO:0004871</td>
</tr> <tr style="border: 1;">
<td>phosphoprotein phosphatase activity</td> <td rowspan="2">hexagon</td> </tr><tr>
<td>GO:0004721</td>
</tr> <tr style="border: 1;">
<td>protein kinase activity</td> <td rowspan="4">octagon</td> </tr><tr>
<td>GO:0004672</td>
</tr> <tr style="border: 1;">
<td>kinase activity</td> </tr><tr>
<td>GO:0016301</td>
</tr> <tr style="border: 1;">
<td>enzyme regulator activity</td> <td rowspan="12">rectangle</td> </tr><tr>
<td>GO:0030234</td>
</tr> <tr style="border: 1;">
<td>chaperone regulator activity</td> </tr><tr>
<td>GO:0030188</td>
</tr> <tr style="border: 1;">
<td>motor activity</td> </tr><tr>
<td>GO:0003774</td>
</tr> <tr style="border: 1;">
<td>RNA binding</td> </tr><tr>
<td>GO:0003723</td>
</tr> <tr style="border: 1;">
<td>DNA binding</td> </tr><tr>
<td>GO:0003677</td>
</tr> <tr style="border: 1;">
<td>nucleic acid binding</td> </tr><tr>
<td>GO:0003676</td>
</tr> <tr style="border: 1;">
<td>hydrolase activity</td> <td rowspan="22">diamond</td> </tr><tr>
<td>GO:0016787</td>
</tr> <tr style="border: 1;">
<td>isomerase activity</td> </tr><tr>
<td>GO:0016853</td>
</tr> <tr style="border: 1;">
<td>lyase activity</td> </tr><tr>
<td>GO:0016829</td>
</tr> <tr style="border: 1;">
<td>aromatase activity</td> </tr><tr>
<td>GO:0008402</td>
</tr> <tr style="border: 1;">
<td>helicase activity</td> </tr><tr>
<td>GO:0004386</td>
</tr> <tr style="border: 1;">
<td>transferase activity</td> </tr><tr>
<td>GO:0016740</td>
</tr> <tr style="border: 1;">
<td>catalytic activity</td> </tr><tr>
<td>GO:0003824</td>
</tr> <tr style="border: 1;">
<td>ligase activity</td> </tr><tr>
<td>GO:0016874</td>
</tr> <tr style="border: 1;">
<td>peptidase activity</td> </tr><tr>
<td>GO:0008233</td>
</tr> <tr style="border: 1;">
<td>oxidoreductase activity</td> </tr><tr>
<td>GO:0016491</td>
</tr> <tr style="border: 1;">
<td>nucleotidyltransferase activity</td> </tr><tr>
<td>GO:0016779</td>
</tr> </tbody>
</table></div>
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<td style="background-color: #993300;color: lightyellow;">Affinity Capture-RNA <span class="b i">(12)</span></td></tr> <tr><td>
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<td style="background-color: #CC3300;color: lightyellow;">Affinity Capture-Western <span class="b i">(39)</span></td></tr> <tr><td>
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<td style="background-color: #000000;color: lightyellow;">Biochemical Activity <span class="b i">(2)</span></td></tr> <tr><td>
<input id="Co-crystalStructure" class="edgeFilter physical" type="checkbox" name="Co-crystalStructure">
</td>
<td style="background-color: #00CC66;color: lightyellow;">Co-crystal Structure <span class="b i">(2)</span></td></tr> <tr><td>
<input id="Co-fractionation" class="edgeFilter physical" type="checkbox" name="Co-fractionation">
</td>
<td style="background-color: #00CC99;color: lightyellow;">Co-fractionation <span class="b i">(0)</span></td></tr> <tr><td>
<input id="Co-localization" class="edgeFilter physical" type="checkbox" name="Co-localization">
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<td style="background-color: #339966;color: lightyellow;">Co-localization <span class="b i">(0)</span></td></tr> <tr><td>
<input id="Co-purification" class="edgeFilter physical" type="checkbox" name="Co-purification">
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<td style="background-color: #FF66CC;color: lightyellow;">Co-purification <span class="b i">(5)</span></td></tr> <tr><td>
<input id="FarWestern" class="edgeFilter physical" type="checkbox" name="FarWestern">
</td>
<td style="background-color: #FF33CC;color: lightyellow;">Far Western <span class="b i">(0)</span></td></tr> <tr><td>
<input id="FRET" class="edgeFilter physical" type="checkbox" name="FRET">
</td>
<td style="background-color: #00FF00;color: lightyellow;">FRET <span class="b i">(2)</span></td></tr> <tr><td>
<input id="PCA" class="edgeFilter physical" type="checkbox" name="PCA">
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<td style="background-color: #00CC66;color: lightyellow;">PCA <span class="b i">(9)</span></td></tr> <tr><td>
<input id="Protein-peptide" class="edgeFilter physical" type="checkbox" name="Protein-peptide">
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<td style="background-color: #9933FF;color: lightyellow;">Protein-peptide <span class="b i">(0)</span></td></tr> <tr><td>
<input id="Protein-RNA" class="edgeFilter physical" type="checkbox" name="Protein-RNA">
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<td style="background-color: #663300;color: lightyellow;">Protein-RNA <span class="b i">(0)</span></td></tr> <tr><td>
<input id="ReconstitutedComplex" class="edgeFilter physical" type="checkbox" name="ReconstitutedComplex">
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<td style="background-color: #FF6699;color: lightyellow;">Reconstituted Complex <span class="b i">(20)</span></td></tr> <tr><td>
<input id="Two-hybrid" class="edgeFilter physical" type="checkbox" name="Two-hybrid">
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<td style="background-color: #CCCCCC;color: lightyellow;">Two-hybrid <span class="b i">(43)</span></td></tr> </tbody>
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filters[$(this).attr('id')] = true;
$(this).attr('checked', true);
});
$('.typeFilter').each(function() {
filters[$(this).attr('id')] = true;
$(this).attr('checked', true);
});
$('.property input').each(function() {
$(this).val(nodeColors[$(this).attr('id')]);
});
}
// init and draw
var vis = new org.cytoscapeweb.Visualization(div_id, options);
function edge_toggle(type) {
filters[type] = !filters[type]; // invert state
var show = filters[type];
vis.filter("edges", function(n) {
var label = n.data.experimentType;
var spaceRegex = / /g;
if (label.replace(spaceRegex,"") == type) {
return show;
} else {
return n.visible;
}
});
}
$(".edgeFilter").change(function() {
edge_toggle($(this).attr('id'));
});
$("#geneticinteractions").change(function(){
var type;
var state = $(this).attr('checked');
$('.genetic').each(function(n) {
if($(this).attr('checked') != state) {
edge_toggle($(this).attr('id'));
$(this).attr('checked', state);
}
});
});
$("#physicalinteractions").change(function(){
var type;
var state = $(this).attr('checked');
$('.physical').each(function(n) {
if($(this).attr('checked') != state) {
edge_toggle($(this).attr('id'));
$(this).attr('checked', state);
}
});
});
function showGo(goInfo, aspect) {
var goRows = "";
for (var i=0; i < goInfo.length; i++) {
var term = goInfo[i];
if (term != aspect) { // skip unknowns
goRows += "<tr><th></th><td>" + term + "</td></tr>";
}
}
if (goRows == "") {
goRows += '<tr><th></th><td><span class="i">Unknown</span></td></tr>';
}
return goRows;
}
function displayGeneProps(info) {
var commonHead = "<table class='summary_mini'><tbody>";
var hasGeneName = false;
if (info.canonicalName != info.systematicName) {
commonHead += "<tr><th>Standard Name</th><td>" + info.canonicalName + "</td></tr>";
hasGeneName = true;
} else {
commonHead += "<tr><th>Systematic Name</th><td>" + info.systematicName + "</td></tr>";
}
basic = commonHead;
if (hasGeneName) {
basic += "<tr><th>Systematic Name</th><td>" + info.systematicName + "</td></tr>";
}
basic += "<tr><th>Name Description</th><td>" + info.geneDescription + "</td></tr>";
var pathways = ""
for (var i=0; i<info.PATHWAY.length; i++) { if(info.PATHWAY[i]) { pathways += "<tr><th></<th><td>" + info.PATHWAY[i] + "</td></tr>";} }
if (pathways != "") {
basic += "<tr><th class='b'>Pathways</th><td></td></tr>";
basic += pathways;
}
basic += "</tbody></table>";
$("#info_basic").html(basic);
var go = commonHead;
go += "<tr><th>"
go += "<tr><th>Molecular Function</th><td></td></tr>" + showGo(info.GO_MOLECULAR_FUNCTION, 'molecular_function');
go += "<tr><th>Biological Process</th><td></td></tr>" + showGo(info.GO_BIOLOGICAL_PROCESS, 'biological_process');
go += "<tr><th>Cellular Component</th><td></td></tr>" + showGo(info.GO_CELLULAR_COMPONENT, 'cellular_component');
go += "</tbody></table>";
$("#info_go").html(go);
var pheno = commonHead;
pheno += "<tr><th class='b'>Phenotypes</th><td></td></tr>"
for (var i=0; i<info.PHENOTYPE.length; i++) { pheno += "<tr><th></th><td>" + info.PHENOTYPE[i] +"</td></tr>";}
pheno += "</tbody></table>";
$("#info_pheno").html(pheno);
}
// utility for pickers
function position_at_input(picker, input){
$(picker).css({
position: "absolute",
left: $(input).offset().left,
top: $(input).offset().top + $(input).outerHeight()
});
if( $(picker).offset().top + $(picker).outerHeight() > $(window).height() ){
$(picker).css({
top: $(input).offset().top - $(picker).outerHeight()
});
}
}
function hide_with_input(picker, input, fn){
if ($(picker).find(".header").is(":visible")) {
// IE set focus to picker, forcing a blur on input, so blur cannot be used here.
// Let's just create a close button instead:
$("#colour_picker .ui-icon-close").bind("click", function(evt){
fn();
evt.preventDefault();
});
} else {
// Regular GOOD browsers!
$(input).bind("blur", function(){
fn();
});
}
$(parent).parent().bind("scroll", function(){
fn();
});
$(window).bind("resize", function(){
fn();
});
}
// add colour pickers
var picker; // parent div to farbtastic
var picker_internals; // farbtastic instance
function remove_picker(){
if( picker != undefined ){
$(picker).remove();
picker = undefined;
picker_internals = undefined;
}
}
function valid_value(value, type){
switch( type ) {
case "colour":
return value.match(/^(\#)([0-9]|[a-f]|[A-F]){6}/);
case "number":
return value.match(/^(-){0,1}([0-9])+((\.)([0-9])+){0,1}/);
case "per cent number":
return value.match(/^((1)|(0)((\.)([0-9])+){0,1})/);
case "integer":
return value.match(/^([0-9])+/);
case "string":
return true;
case "non-empty string":
return value != null && value != "";
case "node shape":
return value.match(/^(ellipse)|(diamond)|(rectangle)|(triangle)|(hexagon)|(roundrect)|(parallelogram)|(octagon)|(vee)|(v)/i);
case "edge shape":
return value.match(/^(circle)|(diamond)|(delta)|(arrow)|(T)|(none)/i);
}
return false;
}
$(document).find(".property input").each(function(){
var input = $(this);
var property = "colour";
nodeColors[$(input).attr('id')] = $(input).val(); // save old value
$(input).addClass("colour_sample_bg");
$(input).validate({
errorMessage: function(str){
return "must be a valid " + property;
},
valid: function(str){
return valid_value( str, property);
}
});
function set_property(viz_objects, filter, value, property) {
// note: viz_objects = "nodes" and property = "color" ignored for now
var style = vis.visualStyle();
vis["customNodeColor"] = function(data) {
if (filter == "ALL_nodes") {
// could also be a visualBypass
return value;
}
for (var i=0;i<data.GO_SLIM_PROCESS.length; i++) {
if (data.GO_SLIM_PROCESS[i] == filter) {
return value;
}
}
// else
return vis.node(data.id).color;
//return "#CCCCCC"; // neutral I guess
}
style.nodes.color = { customMapper: { functionName: "customNodeColor" } };
vis.visualStyle(style);
}
function set_colour(){
$(input).css({
backgroundColor: $(input).val()
});
}
set_colour();
// update colour on picker after typing
$(input).bind("valid", function(){
if( picker_internals != undefined ){
picker_internals.setColor( $(input).val() );
}
set_property( "nodes", $(input).attr("name"), ""+$(input).val(), "fillColor");
set_colour();
});
$(input).bind("invalid", function(){
$(input).css("background-color", "transparent");
});
// on empty put # so user doesn't have to
$(input).bind("keyup", function(){
if( $(this).val() == "" ){
$(this).val("#");
}
});
// add clicker near input when clicked
$(input).bind("click", function(){
remove_picker();
picker = $('<div id="colour_picker" class="floating_widget">' +
'<div class="header ui-state-default"><div class="ui-icon ui-icon-close"/></div><div class="content"/></div>');
$("body").append(picker);
if (!$.browser.msie) { $("#colour_picker .header").hide(); }
picker_internals = $.farbtastic($("#colour_picker .content"), function(colour){
$(input).val(colour).trigger("validate");
});
position_at_input($(picker), $(input));
$(input).trigger("validate");
hide_with_input($(picker), $(input), function(){
remove_picker();
});
});
});
$('input:reset').button();
$('input:reset').click(function() {
vis.draw({layout: {
name: "ForceDirected",
options: {
mass: 300,
gravitation: -500,
tension: 0.1,
restLength: "auto",
drag: 0.4,
iterations: 400 ,
maxTime: 20000 ,
minDistance: 1,
maxDistance: 10000,
autoStabilize: true
}
},
network: xml,
edgeTooltipsEnabled: true,
nodeTooltipsEnabled: true,
});
resetFilters();