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<html>  
<html>  
        <style>
            /* The Cytoscape Web container must have its dimensions set. */
#f5_cytoscapeweb { width: 50%; height:600px; float: left; text-align: center; }
#f5_cytoscapeweb img { vertical-align: middle; }
            #cytoscapeweb { float: left; z-index: 100; width: 100%; height: 500px; }
#loading { position: absolute; top: 0; left: 0;  z-index: 1000; background-image:url("transparentbg.png"); width: 100%; height:100%; min-height: 10em; display: table-cell; vertical-align: middle; text-align: center; }
#loading img { vertical-align: middle; margin: auto; }
#loading p { vertical-align: middle; margin: 200px auto; }
label.style, label.filter, label.export { clear: both; font-weight:bold; display: block; padding-top: 10px; }
table.slider { width: 100%; padding-top: 10px; padding-bottom: 15px; }
#tabs { width: 48%; height:600px; float: right; }
#cyto_recalc { width: 32px; height: 32px; }
#data_bar { position: relative; padding-right: 10px; }
#cyto_zscore_min { width: 35px; text-align: right; padding-right: 10px; }
#cyto_zscore_max { width: 35px; text-align: left; padding-left: 10px; }
#nodes_list, #edges_list { width: 100%; border: 1; }
#properties_panel { font-size: x-small; overflow-y:scroll; }
#properties_panel a { text-decoration:underline; color: #0099ff; }
#properties_panel a.motif { color: #ff9900; }
#properties_panel a.tf { color: #0099ff; }
#properties_panel a.tf_src { color: #0099ff; }
a.ui-slider-handle { outline-style: none; }
a.ui-slider-handle span { float: left; margin-top: 20px;}
        </style>


         <h1 id="firstHeading" class="firstHeading">FF:10717-109I6, TF to Motif to TF network</h1>
         <h1 id="firstHeading" class="firstHeading">FF:10717-109I6, TF to Motif to TF network</h1>
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</p>
</p>


</html>
<html>
<!-- F5 Cytoscape App HTML -->
<div id="f5_cytoscapeweb">
<div id="f5_cytoscapeweb">
<div id="cytoscapeweb"></div>
<div id="tabs_box">
<!-- a href="http://cytoscapeweb.cytoscape.org/">
<div id="tabs">
<img src="http://cytoscapeweb.cytoscape.org/img/logos/cw_s.png" alt="Cytoscape Web"/>
<ul>
</a -->
<li><a href="#style_panel">Layout</a></li>
<li><a href="#filter_panel">Filter</a></li>
<p /><br /><b>LEGEND:</b> <span class="tf">TF <img src="/resource_browser/nwfiles/tf.png" /></span>, <span class="motif">MOTIF <img src="/resource_browser/nwfiles/motif.png" /></span>,
<li><a href="#export_panel">Export</a></li>
<span class="tf">MOTIF->TF <img src="/resource_browser/nwfiles/motif-tf.png" /></span>, <span class="motif">TF->MOTIF <img src="/resource_browser/nwfiles/tf-motif.png" /></span>
<li><a href="#properties_panel_nodes">Nodes</a></li>
<li><a href="#properties_panel_edges">Edges</a></li>
</ul>
<div id="style_panel">
<label class="style">Layout:</label>
<select id="cyto_layout" class="ui-button ui-widget ui-state-default ui-corner-all ui-button-text-only">
  <option value="Preset">Preset</option>
  <option value="ForceDirected" selected>Force Directed</option>
  <option value="Circle">Circle</option>
  <option value="Radial">Radial</option>
  <option value="Tree">Tree</option>
</select>
<button id="cyto_recalc">Recalculate</button>
<label class="style">Labels:</label>
<input type="checkbox" id="cyto_node_labels" checked> Nodes</td></tr>
<br /><input type="checkbox" id="cyto_edge_labels"> Edges</td></tr>
</div>
<div id="filter_panel">
<div>
<label class="filter">Show edges:</label>
<div id="edge_type_filter">
<input type="checkbox" id="cyto_edges_binds_to" value="binds_to" checked>TF->MOTIF</input>
<br /><input type="checkbox" id="cyto_edges_promotes" value="promotes" checked>Promoters</input>
</div>
<div id="z_filter" class="slider">Promoter Z-Score:</div>
 
<p />
<div id="degree_filter" class="slider">Motif degree:</div>
<div id="tf_indegree_filter" class="slider">TF indegree:</div>


</div>
<div id="nodes_type_filter">
<label class="filter">TF outdegree:</label>
<input type="checkbox" id="cyto_nodes_tf_src" value="tf" checked>Source (Outdegree > 0)</input>
<div id="tabs">
<br /><input type="checkbox" id="cyto_nodes_tf" value="tf" checked>Target (Outdegree = 0)</input>
<ul>
</div>
<li><a href="#style_panel">Layout</a></li>
<li><a href="#filter_panel">Filter</a></li>
<li><a href="#export_panel">Export</a></li>
<li><a href="#properties_panel">Data Display</a></li>
</ul>
<div id="style_panel">
<label class="style">Layout:</label>
<select id="cyto_layout" class="ui-button ui-widget ui-state-default ui-corner-all ui-button-text-only">
  <option value="Preset">Preset</option>
  <option value="ForceDirected">Force Directed</option>
  <option value="Circle">Circle</option>
  <option value="Radial">Radial</option>
  <option value="Tree">Tree</option>
</select>
<button id="cyto_recalc">Recalculate</button>
<label class="style">Labels:</label>
<input type="checkbox" id="cyto_node_labels" checked> Nodes</td></tr>
<br /><input type="checkbox" id="cyto_edge_labels"> Edges</td></tr>
</div>
        <div id="filter_panel">
<label class="filter">Z-Score filter:</label>
<table class="slider">
<tr><td></td><td id="data_bar"></td><td></td></tr>
<tr valign="bottom"><td id="cyto_zscore_min" >0.00</td><td ><div id="slider1" class="sliderbar"></div></td><td id="cyto_zscore_max">1</td></tr>
<!-- tr><td></td><td valign="top" ><input type="text" id="cyto_zscore_filter_min" value="0" style="float: left; width: 35px;"/>  <input type="text" id="cyto_zscore_filter_max" value="100" style="float: right; width: 35px;"/></td><td></td></tr -->
</table>
<label class="filter">Show edges:</label>
<input type="checkbox" id="cyto_edges_binds_to" checked>TF->MOTIF</input> <input type="checkbox" id="cyto_edges_promotes" checked>MOTIF->TF</input>
<label class="filter">Show nodes:</label>
<input type="checkbox" id="cyto_nodes_tf_src" checked>Source TF</input> <input type="checkbox" id="cyto_nodes_tf" checked>Target TF</input> <input type="checkbox" id="cyto_nodes_motif" checked>MOTIF</input>


</div>
</div>
<div id="properties_panel_nodes" class="properties_panel scrollable">
<div>
<button id="btn_show_all_nodes" class="rt_btn">Show all nodes</button>
<button id="btn_show_select_nodes" class="rt_btn">Show only selected nodes</button>
<p /><table id="nodes_list" class="wikitable">
</table>
</div>
</div>
<div id="properties_panel_edges" class="properties_panel scrollable">
<div>
<button id="btn_show_all_edges" class="rt_btn">Show all edges</button>
<button id="btn_show_select_edges" class="rt_btn">Show only selected edges</button>
<p /><table id="edges_list" class="wikitable">
</table>
</div>
</div>
<div id="export_panel">
<label class="export">Export Network:</label>
  <button id="btn_exportGraphml">graphml</button>
  <button id="btn_exportXgmml">xgmml</button>
  <button id="btn_exportSIF">sif</button>
  <button id="btn_exportJSON">JSON</button>
<label class="export">Export Image:</label>
  <button id="btn_exportPDF">PDF</button>
  <button id="btn_exportPNG">PNG</button>
  <button id="btn_exportSVG">SVG</button>
</div>
</div>
</div>
<div id="properties_panel" style="height: 540px;">
<div>
<table id="nodes_list" class="wikitable">
</table>
</div>
<div>
<table id="edges_list" class="wikitable">
</table>
</div>
        </div>
<div id="export_panel">
<label class="export">Export Network:</label>
<button id="btn_exportGraphml">graphml</button>
<button id="btn_exportXgmml">xgmml</button>
<button id="btn_exportSIF">sif</button>
<button id="btn_exportJSON">JSON</button>
<label class="export">Export Image:</label>
<button id="btn_exportPDF">PDF</button>
<button id="btn_exportPNG">PNG</button>
<button id="btn_exportSVG">SVG</button>
</div>
</div>
</div>


<div id="cytoscapeweb"></div>
<div id="legend"><b>LEGEND:</b> <span class="tf">TF <img src="/resource_browser/nwfiles/tf.png" /></span>, <span class="motif">MOTIF <img src="/resource_browser/nwfiles/motif.png" /></span>,
<br /><span class="tf">MOTIF->TF <img src="/resource_browser/nwfiles/motif-tf.png" /></span>, <span class="motif">TF->MOTIF <img src="/resource_browser/nwfiles/tf-motif.png" /></span></div>
</div>
<!-- Header Section -->
<!-- JQuery UI -->
<!-- JQuery UI -->
<script type="text/javascript" src="/resource_browser/nwfiles/jquery-ui.min.js"></script>
<script type="text/javascript" src="/resource_browser/nwfiles/jquery-ui.min.js"></script>
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         <script type="text/javascript" src="/resource_browser/rb_js/cytoscapeweb/js/min/cytoscapeweb.min.js"></script>
         <script type="text/javascript" src="/resource_browser/rb_js/cytoscapeweb/js/min/cytoscapeweb.min.js"></script>


     
<!-- F5 Cytoscape app -->
<link href="/resource_browser/nwfiles/f5_cytoview_2.css" rel="stylesheet"/>
        <script type="text/javascript" src="/resource_browser/nwfiles/f5_cytoview_5.js"></script>
 
<!-- Data Loading Section -->
<script type="text/javascript">
<script type="text/javascript">
// Load Data
// Load Data
var durl = "/resource_browser/nwfiles/10717-109I6.xgmml";
//var durl = "/resource_browser/nwfiles/</html>{{{CNhs}}}.{{{FFid}}}.xgmml<html>";
                var durl = "/resource_browser/nwfiles/CNhs10630.10024-101D6.xgmml"


//$.get(durl, function(data) {
//$.get(durl, function(data) {
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};
};
</script>
</script>
<script type="text/javascript" src="/resource_browser/nwfiles/f5_cytoview_3.js"></script>


</html>
</html>

Latest revision as of 11:28, 20 July 2012

FF:10717-109I6, TF to Motif to TF network

Mouseover nodes and edges to see attributes. Motifs are shown in orange, TFs are shown in blue. Promoter and z-score are attributes of the Motif to TF edges (blue arrow). TF to Motif edges are shown in orange.

Motifs shown are the top (maximum 30) motifs in the sample. TFs shown have at least one CAGE promoter with at at least 10 TPM expression (RLE normalized) in the sample. Edges shown have a z-score of at least 1.5 (based on correlation between motif activity and promoter expression).

Nodes
Edges
TF->MOTIF
Promoters
Promoter Z-Score:

Motif degree:
TF indegree:
Source (Outdegree > 0)
Target (Outdegree = 0)

LEGEND: TF , MOTIF ,
MOTIF->TF , TF->MOTIF

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