Template:Tf motif cytoscapenw
From FANTOM5_SSTAR
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>
<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); });
