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<html><link rel="stylesheet" href="/resource_browser/nwfiles/f5-style.css" /></html>
<html><link rel="stylesheet" href="/resource_browser/nwfiles/css/f5-style.css" /></html>
<html>  
<html>  


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<div id="cytoscapeweb"></div>
<div id="cytoscapeweb"></div>
<div id="legend">
<div id="legend">
<div id="node_legend">
<div id="node_legend">
TF <div class="node tf sampleA"></div>, MOTIF <div class="node motif sampleA"></div>  
<table>
<tr>
<td>SAMPLE</td>
<td><svg width="20" height="24">
<circle r="10" cx="10" cy="14" class="tf"/>
</svg>
TF</td>
<td><svg width="20" height="24">
<rect width="20" height="20" x="0" y="4" class="motif"/>
</svg>
MOTIF</td>
</tr>
</table>
</div>
</div>
<div id="edge_legend">
<div id="edge_legend">
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<li><a href="#properties_panel_edges">Edges</a></li>
<li><a href="#properties_panel_edges">Edges</a></li>
<li><a href="#compare_panel">Compare</a></li>
<li><a href="#compare_panel">Compare</a></li>
<li><a href="#help_panel">Help</a></li>
</ul>
</ul>
<div id="style_panel">
<div id="style_panel">
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<input type="text" class="left" id="samples" name="blah" title="Search" />
<input type="text" class="left" id="samples" name="blah" title="Search" />
<button id="cyto_load" class="right">Load</button>
<button id="cyto_load" class="right">Load</button>
<div>
</div>
<p />
<p />
<div id="sample_filter">
<div id="sample_filter">
<br><input type="radio" name="sample" value="" checked>Union: A || B
<br><input type="radio" name="sample" value="" checked>Union: A || B
<br><input type="radio" name="sample" value=",">Intersection: A && B
<br><input type="radio" name="sample" value=",">Intersection: A &amp;&amp; B
<br><input type="radio" name="sample" value="^_A$">Difference: A - B
<br><input type="radio" name="sample" value="^_A$">Difference: A - B
<br><input type="radio" name="sample" value="^_B$">Difference: B - A
<br><input type="radio" name="sample" value="^_B$">Difference: B - A
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<br><input type="radio" name="sample" value="_B">Subnetwork: B
<br><input type="radio" name="sample" value="_B">Subnetwork: B
</div>
</div>
</div>
<div id="help_panel">
<h3>About this network view.</h3>
<p>
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).
</p>
<p>
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>
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<link href="//ajax.googleapis.com/ajax/libs/jqueryui/1.8.10/themes/redmond/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/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"/>
<link href="/resource_browser/nwfiles/css/f5_cytoview_7.min.css" rel="stylesheet"/>
<link href="/resource_browser/nwfiles/js/multiselect/css/ui.multiselect.css" rel="stylesheet"/>


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


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         <!-- Cytoscape Web JS API (needed to reference org.cytoscapeweb.Visualization) -->
         <!-- Cytoscape Web JS API (needed to reference org.cytoscapeweb.Visualization) -->
         <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 -->
<script type="text/javascript" src="/resource_browser/nwfiles/js/encode_decode.js"></script>
         <script type="text/javascript" src="/resource_browser/nwfiles/js/f5_cytoview_6.js"></script>


<!-- Data Loading Section -->
<!-- Data Loading Section -->
<script type="text/javascript">
<script type="text/javascript">
$(document).ready(function() {


// Options for FANTOM5 Network view app
// Options for FANTOM5 Network view app
var f5_options = {
var o = {
  networkPath: '/resource_browser/nwfiles/tfnetworks/',
  networkPath: '/resource_browser/nwfiles/tfnetworks/',
  initSample: 'CNhs10746.10429-106D6',
  initSample: 'CNhs10746.10429-106D6',
  samplesPath: '/resource_browser/nwfiles/js/hg19_samples.json',
  swfPath: "/resource_browser/rb_js/cytoscapeweb/swf/CytoscapeWeb",
  swfPath: "/resource_browser/rb_js/cytoscapeweb/swf/CytoscapeWeb",
  flashInstallerPath: "/resource_browser/rb_js/cytoscapeweb/swf/playerProductInstall"
  flashInstallerPath: "/resource_browser/rb_js/cytoscapeweb/swf/playerProductInstall",
  linkOutPath: "/resource_browser/RB_SearchResults?sq="
}
}
riken.f5_network_vis.start(o);
});
</script>
</script>
<script type="text/javascript" src="/resource_browser/nwfiles/js/f5_cytoview_7.min.js"></script>


</html>
</html>

Latest revision as of 09:50, 4 September 2012

Details

Transcriptome profiling

hCAGE {{{profile_hcage}}}
RNA-seq {{{profile_rnaseq}}}
smallRNA seq {{{profile_srnaseq}}}
nanoCAGEscan {{{profile_cagescan}}}

Sample info

strain {{{sample_strain}}}
tissue {{{sample_tissue}}}
dev_stage {{{sample_dev_stage}}}
sex {{{sample_sex}}}
age {{{sample_age}}}
ethnicity {{{sample_ethnicity}}}
cell_type {{{sample_cell_type}}}
cell_line {{{sample_cell_line}}}
collaboration {{{sample_collaboration}}}
Experimental condition{{{sample_experimental_condition}}}
disease {{{sample_disease}}}
cell_lot {{{sample_cell_lot}}}
cell_catalog {{{sample_cell_catalog}}}
company {{{sample_company}}}
donor(cell lot) {{{sample_donor(cell lot)}}}
Note {{{sample_note}}}


RNA info

sample_id {{{sample_id}}}
tube_id {{{rna_tube_id}}}
box {{{rna_box}}}
position {{{rna_position}}}
lot_number {{{rna_lot_number}}}
catalog_number {{{rna_catalog_number}}}
RIN {{{rna_rin}}}
OD260/230 {{{rna_od260/230}}}
OD260/280 {{{rna_od260/280}}}
sample_type {{{rna_sample_type}}}
extraction_protocol {{{rna_extraction_protocol}}}
weight_ug {{{rna_weight_ug}}}
concentration{{{rna_concentration}}}


SAMPLE TF MOTIF
Promoter
TF-MOTIF Binding
Nodes
Edges
TF-MOTIF Binding
Promoters
Promoter Z-Score filter:

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


Union: A || B
Intersection: A && B
Difference: A - B
Difference: B - A
Subnetwork: A
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