Personal tools

Cytoscape test3: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(5 intermediate revisions by the same user not shown)
Line 27: Line 27:
<select id="cyto_layout" class="ui-button ui-widget ui-state-default ui-corner-all ui-button-text-only">
<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="Preset">Preset</option>
  <option value="ForceDirected">Force Directed</option>
  <option value="ForceDirected" selected>Force Directed</option>
  <option value="Circle">Circle</option>
  <option value="Circle">Circle</option>
  <option value="Radial">Radial</option>
  <option value="Radial">Radial</option>
Line 38: Line 38:
</div>
</div>
<div id="filter_panel">
<div id="filter_panel">
<div>
<label class="filter">Show edges:</label>
<label class="filter">Show edges:</label>
<input type="checkbox" id="cyto_edges_binds_to" checked>TF->MOTIF</input>
<div id="edge_type_filter">
<br /><input type="checkbox" id="cyto_edges_promotes" checked>Promoters</input>
<input type="checkbox" id="cyto_edges_binds_to" value="binds_to" checked>TF->MOTIF</input>
<label class="filter">Z-Score filter:</label>
<br /><input type="checkbox" id="cyto_edges_promotes" value="promotes" checked>Promoters</input>
<table class="slider">
</div>
<tr><td></td><td><div id="data_bar"></div></td><td></td></tr>
<div id="z_filter" class="slider">Promoter Z-Score:</div>
<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>
 
</table>
<label class="filter">Show nodes:</label>
<input type="checkbox" id="cyto_nodes_tf_src" checked>Source TF (Outdegree = 1)</input>
<br /><input type="checkbox" id="cyto_nodes_tf" checked>Target TF (Outdegree = 0)</input>
<br /><input type="checkbox" id="cyto_nodes_motif" checked>MOTIF</input>
<p />
<p />
<div id="degree_filter" class="slider">Motif degree:</div>
<div id="tf_indegree_filter" class="slider">TF indegree:</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>
<br /><input type="checkbox" id="cyto_nodes_tf" value="tf" checked>Target (Outdegree = 0)</input>
</div>
</div>
</div>
</div>
<div id="properties_panel_nodes" class="properties_panel">
<div id="properties_panel_nodes" class="properties_panel scrollable">
<div>
<div>
<button id="btn_show_select_nodes" class="rt_btn">Show only these nodes</button>
<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">
<p /><table id="nodes_list" class="wikitable">
</table>
</table>
</div>
</div>
</div>
</div>
<div id="properties_panel_edges" class="properties_panel">
<div id="properties_panel_edges" class="properties_panel scrollable">
<div>
<div>
<button id="btn_show_select_edges" class="rt_btn">Show only these edges</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>
<p /><table id="edges_list" class="wikitable">
<p /><table id="edges_list" class="wikitable">
</table>
</table>
Line 104: Line 113:


<!-- F5 Cytoscape app -->
<!-- F5 Cytoscape app -->
<link href="/resource_browser/nwfiles/f5_cytoview.css" rel="stylesheet"/>
<link href="/resource_browser/nwfiles/f5_cytoview_2.css" rel="stylesheet"/>
         <script type="text/javascript" src="/resource_browser/nwfiles/f5_cytoview_4.js"></script>  
         <script type="text/javascript" src="/resource_browser/nwfiles/f5_cytoview_5.js"></script>  


<!-- Data Loading Section -->
<!-- Data Loading Section -->
Line 111: Line 120:
// Load Data
// Load Data
//var durl = "/resource_browser/nwfiles/</html>{{{CNhs}}}.{{{FFid}}}.xgmml<html>";
//var durl = "/resource_browser/nwfiles/</html>{{{CNhs}}}.{{{FFid}}}.xgmml<html>";
                 var durl = "/resource_browser/nwfiles/CNhs10652.10045-101F9.xgmml"
                 var durl = "/resource_browser/nwfiles/CNhs10630.10024-101D6.xgmml"


//$.get(durl, function(data) {
//$.get(durl, function(data) {

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