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<html>
<!-- F5 Cytoscape App HTML -->
<!-- F5 Cytoscape App HTML -->
<div id="f5_cytoscapeweb">
<div id="f5_cytoscapeweb">
<div id="tabs_box">
<div id="panel1">
<div id="tabs">
<h2 id="cyto_title"></h2>
<ul>
<div id="cytoscapeweb"></div>
<li><a href="#style_panel">Layout</a></li>
<div id="legend">
<li><a href="#filter_panel">Filter</a></li>
<div id="node_legend">
<li><a href="#export_panel">Export</a></li>
TF <div class="node tf sampleA"></div>, MOTIF <div class="node motif sampleA"></div>  
<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>
<div id="filter_panel">
<div id="edge_legend">
<div>
Promoter <img src="/resource_browser/nwfiles/img/motif-tf.png" />
<label class="filter">Show edges:</label>
<br />TF-MOTIF Binding <img src="/resource_browser/nwfiles/img/tf-motif.png" />
<div id="edge_type_filter">
</div>
<input type="checkbox" id="cyto_edges_binds_to" value="binds_to" checked>TF->MOTIF</input>
</div>
<br /><input type="checkbox" id="cyto_edges_promotes" value="promotes" checked>Promoters</input>
</div>
<div id="panel2">
<div id="tabs">
<ul>
<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_nodes">Nodes</a></li>
<li><a href="#properties_panel_edges">Edges</a></li>
<li><a href="#compare_panel">Compare</a></li>
<li><a href="#help_panel">Help</a></li>
</ul>
<div id="style_panel">
<label class="style">Layout:</label>
<select id="cyto_layout" style="float: left;" 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>
<div id="show_labels">
<input type="checkbox" id="cyto_node_labels" checked> Nodes
<br /><input type="checkbox" id="cyto_edge_labels"> Edges
</div>
</div>
</div>
<div id="z_filter" class="slider">Promoter Z-Score:</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 Binding</input>
<br /><input type="checkbox" id="cyto_edges_promotes" value="promotes" checked>Promoters</input>
</div>
<div id="z_filter" class="slider">Promoter Z-Score filter:</div>


<p />
<p />
<!-- div id="degree_filter" class="slider">Motif degree:</div -->
<div id="degree_filter" class="slider">Motif degree filter:</div>
<div id="tf_indegree_filter" class="slider">TF indegree:</div>
<div id="tf_indegree_filter" class="slider">TF indegree filter:</div>
 
<div id="nodes_type_filter">
<div id="nodes_type_filter">
<label class="filter">TF outdegree:</label>
<label class="filter">TF outdegree filter:</label>
<input type="checkbox" id="cyto_nodes_tf_src" value="tf" checked>Source (Outdegree > 0)</input>
<input type="checkbox" id="cyto_nodes_tf_src" value="tf" checked>Source TF (Outdegree > 0)</input>
<br /><input type="checkbox" id="cyto_nodes_tf" value="tf" checked>Target (Outdegree = 0)</input>
<br /><input type="checkbox" id="cyto_nodes_tf" value="tf" checked>Target TF (Outdegree = 0)</input>
</div>
</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>
 
<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="compare_panel">
<div id="properties_panel_nodes" class="properties_panel scrollable">
<div id="load">
<div>
<input type="text" class="left" id="samples" name="blah" title="Search" />
<button id="btn_show_all_nodes" class="rt_btn">Show all nodes</button>
<button id="cyto_load" class="right">Load</button>
<button id="btn_show_select_nodes" class="rt_btn">Show only selected nodes</button>
</div>
<p /><table id="nodes_list" class="wikitable">
<p />
</table>
<div id="sample_filter">
<br><input type="radio" name="sample" value="" checked>Union: A || B
<br><input type="radio" name="sample" value=",">Intersection: A &amp;&amp; B
<br><input type="radio" name="sample" value="^_A$">Difference: A - B
<br><input type="radio" name="sample" value="^_B$">Difference: B - A
<br><input type="radio" name="sample" value="_A">Subnetwork: A
<br><input type="radio" name="sample" value="_B">Subnetwork: B
</div>
</div>
</div>
</div>
<div id="help_panel">
<div id="properties_panel_edges" class="properties_panel scrollable">
<h3>About this network view.</h3>
<div>
<p>
<button id="btn_show_all_edges" class="rt_btn">Show all edges</button>
Motifs shown are the top motifs in the sample (maximum 30). 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).
<button id="btn_show_select_edges" class="rt_btn">Show only selected edges</button>
</p>
<p /><table id="edges_list" class="wikitable">
<p>
</table>
In the single sample view 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.
</p>
<h3>How to interact with the network?</h3>
<p>
Zoom using the control panel in the lower right.
<br />Click and drag to move nodes.
<br />Double click to search for label in resource browser.
<br />Mouse over nodes and edges to see additional attributes.
<br />Hover over a node to highlight its first neighbors.
<br />Click and drag or shift-click on the canvas to highlight many nodes and edges.
<br />Right click on a node to select its first neighbors.
<br />Right click to show only selected nodes.
<br />When nodes are selected additional information is available in the pull out panel.
<br />Addition filters are available within the pull out panel.
</p>
<h3>Acknowledgments</h3>
<p>
Analyst: Erik Arner
<br />Application Developer: Jayson Harshbarger
<p>
Research Grant for RIKEN Omics Science Center from MEXT to Yoshihide Hayashizaki
<br />Grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to Yoshihide Hayashizaki
</p>
</p>
</div>
</div>
</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>
</div>
<!-- Header Section -->
<!-- CSS (To ensure CSS files are downloaded in parallel, always include external CSS before external JavaScript.) -->
<link href="//ajax.googleapis.com/ajax/libs/jqueryui/1.8.10/themes/base/jquery-ui.css" rel="stylesheet" />
<link href="//ajax.googleapis.com/ajax/libs/jqueryui/1.8.10/themes/redmond/jquery-ui.css" rel="stylesheet" />
<link href="/resource_browser/nwfiles/js/wijmo/jquery.wijmo-complete.all.2.1.4.min.css" rel="stylesheet" type="text/css" />
<link href="/resource_browser/nwfiles/css/f5_cytoview_3.css" rel="stylesheet"/>


<div id="cytoscapeweb"></div>
<!-- JQuery -->
<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>,
<!-- script type="text/javascript" src="//ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script -->
<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>
<script src="/resource_browser/nwfiles/js/jquery.ba-throttle-debounce.min.js" type="text/javascript"></script>


<!-- JQuery UI -->
<script type="text/javascript" src="//ajax.googleapis.com/ajax/libs/jqueryui/1.8.18/jquery-ui.min.js"></script>


</div>
<!-- wWijmo Widgets -->
<script src="/resource_browser/nwfiles/js/wijmo/jquery.wijmo-open.all.2.1.4.min.js" type="text/javascript"></script>


<!-- Header Section -->
<!-- tokeninput -->
<!-- JQuery UI -->
<script type="text/javascript" src="/resource_browser/nwfiles/js/jquery.tokeninput.js"></script>
<script type="text/javascript" src="/resource_browser/nwfiles/jquery-ui.min.js"></script>
<link href="//ajax.googleapis.com/ajax/libs/jqueryui/1.8.10/themes/base/jquery-ui.css" rel="stylesheet" />
<link href="//ajax.googleapis.com/ajax/libs/jqueryui/1.8.10/themes/redmond/jquery-ui.css" rel="stylesheet" />


         <!-- JSON support for IE (needed to use JS API) -->
         <!-- JSON support for IE (needed to use JS API) -->
Line 103: Line 170:


<!-- F5 Cytoscape app -->
<!-- F5 Cytoscape app -->
<link href="/resource_browser/nwfiles/f5_cytoview_2.css" rel="stylesheet"/>
<script type="text/javascript" src="/resource_browser/nwfiles/js/encode_decode.js"></script>  
        <script type="text/javascript" src="/resource_browser/nwfiles/f5_cytoview_5.js"></script>  
       


<!-- Data Loading Section -->
<!-- Data Loading Section -->
<script type="text/javascript">
<script type="text/javascript">
// Load Data
var durl = "/resource_browser/nwfiles/</html>{{{CNhs}}}.{{{FFid}}}.xgmml<html>";
                //var durl = "/resource_browser/nwfiles/CNhs10630.10024-101D6.xgmml"


var request = new XMLHttpRequest();
$(document).ready(function() {
request.open("GET", durl , false);
 
request.send(null);
// Options for FANTOM5 Network view app
var xml = request.responseText;
var f5_options = {
  networkPath: '/resource_browser/nwfiles/tfnetworks/',
  initSample: '</html>{{{CNhs}}}.{{{FFid}}}<html>',
  swfPath: "/resource_browser/rb_js/cytoscapeweb/swf/CytoscapeWeb",
  flashInstallerPath: "/resource_browser/rb_js/cytoscapeweb/swf/playerProductInstall",
  linkOutPath: "/resource_browser/RB_SearchResults?sq="
}


// initialization cytoscape options
f5_start(f5_options);
var options = {
});
swfPath: "/resource_browser/rb_js/cytoscapeweb/swf/CytoscapeWeb",
flashInstallerPath: "/resource_browser/rb_js/cytoscapeweb/swf/playerProductInstall"
};
</script>
</script>
<script type="text/javascript" src="/resource_browser/nwfiles/js/f5_cytoview_6.js"></script>


</html>
</html>

Revision as of 14:22, 15 August 2012

TF
, MOTIF

Promoter <img src="/resource_browser/nwfiles/img/motif-tf.png" />
TF-MOTIF Binding <img src="/resource_browser/nwfiles/img/tf-motif.png" />

  • <a href="#style_panel">Layout</a>
  • <a href="#filter_panel">Filter</a>
  • <a href="#export_panel">Export</a>
  • <a href="#properties_panel_nodes">Nodes</a>
  • <a href="#properties_panel_edges">Edges</a>
  • <a href="#compare_panel">Compare</a>
  • <a href="#help_panel">Help</a>

<label class="style">Layout:</label> <select id="cyto_layout" style="float: left;" class="ui-button ui-widget ui-state-default ui-corner-all ui-button-text-only"> <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
<input type="checkbox" id="cyto_edge_labels"> Edges

<label class="filter">Show edges:</label>

<input type="checkbox" id="cyto_edges_binds_to" value="binds_to" checked>TF-MOTIF Binding</input>
<input type="checkbox" id="cyto_edges_promotes" value="promotes" checked>Promoters</input>

Promoter Z-Score filter:

Motif degree filter:
TF indegree filter:

<label class="filter">TF outdegree filter:</label> <input type="checkbox" id="cyto_nodes_tf_src" value="tf" checked>Source TF (Outdegree > 0)</input>
<input type="checkbox" id="cyto_nodes_tf" value="tf" checked>Target TF (Outdegree = 0)</input>

<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>

<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>

<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>

<input type="text" class="left" id="samples" name="blah" title="Search" /> <button id="cyto_load" class="right">Load</button>


<input type="radio" name="sample" value="" checked>Union: A || B
<input type="radio" name="sample" value=",">Intersection: A && B
<input type="radio" name="sample" value="^_A$">Difference: A - B
<input type="radio" name="sample" value="^_B$">Difference: B - A
<input type="radio" name="sample" value="_A">Subnetwork: A
<input type="radio" name="sample" value="_B">Subnetwork: B

About this network view.

Motifs shown are the top motifs in the sample (maximum 30). 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).

In the single sample view 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.

How to interact with the network?

Zoom using the control panel in the lower right.
Click and drag to move nodes.
Double click to search for label in resource browser.
Mouse over nodes and edges to see additional attributes.
Hover over a node to highlight its first neighbors.
Click and drag or shift-click on the canvas to highlight many nodes and edges.
Right click on a node to select its first neighbors.
Right click to show only selected nodes.
When nodes are selected additional information is available in the pull out panel.
Addition filters are available within the pull out panel.

Acknowledgments

Analyst: Erik Arner
Application Developer: Jayson Harshbarger

Research Grant for RIKEN Omics Science Center from MEXT to Yoshihide Hayashizaki
Grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to Yoshihide Hayashizaki

<link href="//ajax.googleapis.com/ajax/libs/jqueryui/1.8.10/themes/base/jquery-ui.css" rel="stylesheet" /> <link href="//ajax.googleapis.com/ajax/libs/jqueryui/1.8.10/themes/redmond/jquery-ui.css" rel="stylesheet" /> <link href="/resource_browser/nwfiles/js/wijmo/jquery.wijmo-complete.all.2.1.4.min.css" rel="stylesheet" type="text/css" /> <link href="/resource_browser/nwfiles/css/f5_cytoview_3.css" rel="stylesheet"/>

<script src="/resource_browser/nwfiles/js/jquery.ba-throttle-debounce.min.js" type="text/javascript"></script>

<script type="text/javascript" src="//ajax.googleapis.com/ajax/libs/jqueryui/1.8.18/jquery-ui.min.js"></script>

<script src="/resource_browser/nwfiles/js/wijmo/jquery.wijmo-open.all.2.1.4.min.js" type="text/javascript"></script>

<script type="text/javascript" src="/resource_browser/nwfiles/js/jquery.tokeninput.js"></script> 

       <script type="text/javascript" src="/resource_browser/rb_js/cytoscapeweb/js/min/json2.min.js"></script>
       
       <script type="text/javascript" src="/resource_browser/rb_js/cytoscapeweb/js/min/AC_OETags.min.js"></script>
       
       <script type="text/javascript" src="/resource_browser/rb_js/cytoscapeweb/js/min/cytoscapeweb.min.js"></script>

<script type="text/javascript" src="/resource_browser/nwfiles/js/encode_decode.js"></script>


<script type="text/javascript">

$(document).ready(function() {

// Options for FANTOM5 Network view app var f5_options = { networkPath: '/resource_browser/nwfiles/tfnetworks/', initSample: '</html>{{{CNhs}}}.{{{FFid}}}', swfPath: "/resource_browser/rb_js/cytoscapeweb/swf/CytoscapeWeb", flashInstallerPath: "/resource_browser/rb_js/cytoscapeweb/swf/playerProductInstall", linkOutPath: "/resource_browser/RB_SearchResults?sq=" } f5_start(f5_options); });

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