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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<title>A developmental gene co-expression network of mouse pancreatic beta cells (BETA-GCN Explorer - Mark Magnuson Lab)</title>
<meta name="description" content="Explore gene expression profiles of a mouse developmental gene co-expression network of pancreatic beta cells"/>
<meta name="keywords" content="Pancreas, pancreatic, beta cells, co-expression network, genes, expression, explore, data, RNA-Seq, modules, meta-modules, iterativeWGCNA, WGCNA, Mark Magnuson">
<meta name="author" content="Jean-Philippe Cartailler">
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<body>
<div class="container-fluid">
<div class="navbar navbar-default navbar-inverse">
<div class="navbar-header">
<span class="navbar-brand">BetaCell-GCN Explorer</span>
</div>
<ul class="nav navbar-nav">
<li class="active"><a href="index.html"> Overview</a></li>
<li><a href="genebrowser/index.html"> Gene Membership & expression</a></li>
<li><a href="genebrowser/modules.html"> Module Statistics</a></li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li><a href="https://github.com/cstoeckert/iterativeWGCNA"> <i class="fab fa-github"></i> iterativeWGCNA</a></li>
</ul>
</div>
<div class="container-fluid">
<div class="row">
<div class="col-sm-12">
<div class="well" style="background: #fff; box-shadow: 0 4px 6px -1px rgba(0, 0, 0, 0.1), 0 2px 4px -1px rgba(0, 0, 0, 0.06);">
<div class="row">
<div class="col-sm-6">
<p>A developmental lineage-based gene co-expression network for mouse pancreatic beta-cells</p>
<img src="images/metanetwork.png" alt="Mouse Pancreas Developmental Network - Osipovich et al" class="pull-right img-responsive">
</div>
<div class="col-sm-6">
<p>Each node in the meta-network represents a module of highly co-expressed genes. The meta-network is defined by correlations between module eigengenes and partitions modules into three distinct strongly connected module groups. See figure 1 in the manuscript for additional detail.
</p>
<ul>
<li><a href="images/metanetwork.png">Download large metanetwork image</a></li>
<li><a href="BetaCell-metanetwork.cys">Download metanetwork Cytoscape file</a></li>
<li><a href="genebrowser/index.html">Browse/search gene expression data</a></li>
<li><a href="genebrowser/modules.html">Browse/search module data</a></li>
</ul>
<p>Please cite:</p>
<blockquote style="font-size:90% !important;">Anna B Osipovich, Karrie D Dudek, Emily Greenfest-Allen, Jean-Philippe Cartailler, Elisabetta Manduchi, Leah Potter Case, Eunyoung Choi, Austin G Chapman, Hannah Worchel Clayton, Guogiang Gu, Christian J Stoeckert, and Mark A Magnuson. A developmental lineage-based gene co-expression network for mouse pancreatic β-cells reveals a role for Zfp800 in pancreas development. Development 2021 .doi: 10.1242/dev.196964 (<a href="https://dev.biologists.org/content/early/2021/02/26/dev.196964">PDF</a>)</blockquote>
</div>
</div>
</div>
<h2>For Biologists</h2>
<p>We have prepared Cytoscape *session* files that you can download and simply open with <a href="https://www.cytoscape.org">Cytoscape</a> to view and interact with the network meta-modules.</p>
<ul>
<li>Option 1 - <a class="button" href="BetaCell-GCN-all-genes.cys">Download Cytoscape file for all genes</a></li>
<li>Option 2 - <a class="button" href="BetaCell-GCN-transcription-factors.cys">Download Cytoscape file for "TF" genes</a>, filtered via <em>transcription factor activity, sequence-specific DNA binding</em> (<a href="http://www.informatics.jax.org/vocab/gene_ontology/GO:0003700">GO:0003700</a>)</li>
</ul>
Once you have downloaded the file, open it with Cytoscape and click on the meta-module of interest in the left sidepanel to load and view it. You can then explore the network via Cytoscape's functionality.
<h2>For Bioinformaticians</h2>
<p>For each meta-module, you will find below:</p>
<ul>
<li>Network image for "all genes" meta-modules</li>
<li>Statistics about number of nodes and edges for "all genes" meta-modules</li>
<li>Cytoscape JSON network file (compressed via ZIP) for all genes</li>
<li>Cytoscape JSON network file (compressed via ZIP) for all genes filtered via **transcription factor activity, sequence-specific DNA binding** (<a href="http://www.informatics.jax.org/vocab/gene_ontology/GO:0003700">GO:0003700</a>)</li>
</ul>
<table class="table table-striped table-bordered" >
<thead>
<tr>
<th>Meta-module</th>
<th>Image</th>
<th># nodes<sup>1</sup></th>
<th># of edges<sup>2</sup></th>
<th>All Genes</th>
<th>Transcription Factors Activity Genes</th>
</tr>
</thead>
<tbody>
<tr>
<td>A</td>
<td><a href="images/metamodule-A.png"><img src="images/metamodule-A_crop_resize.jpg" alt="Meta-module A" style="max-width:100%;"></a></td>
<td>103</td>
<td>732</td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-A_filterlevel-any.zip">Download</a></td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-A_filterlevel-any_tfOnly.zip">Download</a></td>
</tr>
<tr>
<td>B</td>
<td><a href="images/metamodule-B.png"><img src="images/metamodule-B_crop_resize.jpg" alt="Meta-module B" style="max-width:100%;"></a></td>
<td>1,039</td>
<td>64,306</td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-B_filterlevel-any.zip">Download</a></td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-B_filterlevel-any_tfOnly.zip">Download</a></td>
</tr>
<tr>
<td>C</td>
<td><a href="images/metamodule-C.png"><img src="images/metamodule-C_crop_resize.jpg" alt="Meta-module C" style="max-width:100%;"></a></td>
<td>3,070</td>
<td>546,028</td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-C_filterlevel-any.zip">Download</a></td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-C_filterlevel-any_tfOnly.zip">Download</a></td>
</tr>
<tr>
<td>D</td>
<td><a href="images/metamodule-D.png"><img src="images/metamodule-D_crop_resize.jpg" alt="Meta-module D" style="max-width:100%;"></a></td>
<td>1,096</td>
<td>65,970</td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-D_filterlevel-any.zip">Download</a></td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-D_filterlevel-any_tfOnly.zip">Download</a></td>
</tr>
<tr>
<td>E</td>
<td><a href="images/metamodule-E.png"><img src="images/metamodule-E_crop_resize.jpg" alt="Meta-module E" style="max-width:100%;"></a></td>
<td>30</td>
<td>56</td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-E_filterlevel-any.zip">Download</a></td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-E_filterlevel-any_tfOnly.zip">Download</a></td>
</tr>
<tr>
<td>F</td>
<td><a href="images/metamodule-F.png"><img src="images/metamodule-F_crop_resize.jpg" alt="Meta-module F" style="max-width:100%;"></a></td>
<td>869</td>
<td>42,414</td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-F_filterlevel-any.zip">Download</a></td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-F_filterlevel-any_tfOnly.zip">Download</a></td>
</tr>
<tr>
<td>G</td>
<td><a href="images/metamodule-G.png"><img src="images/metamodule-G_crop_resize.jpg" alt="Meta-module G" style="max-width:100%;"></a></td>
<td>54</td>
<td>177</td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-G_filterlevel-any.zip">Download</a></td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-G_filterlevel-any_tfOnly.zip">Download</a></td>
</tr>
<tr>
<td>H</td>
<td><a href="images/metamodule-H.png"><img src="images/metamodule-H_crop_resize.jpg" alt="Meta-module H" style="max-width:100%;"></a></td>
<td>226</td>
<td>2,927</td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-H_filterlevel-any.zip">Download</a></td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-H_filterlevel-any_tfOnly.zip">Download</a></td>
</tr>
<tr>
<td>I</td>
<td><a href="images/metamodule-I.png"><img src="images/metamodule-I_crop_resize.jpg" alt="Meta-module I" style="max-width:100%;"></a></td>
<td>246</td>
<td>3,549</td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-I_filterlevel-any.zip">Download</a></td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-I_filterlevel-any_tfOnly.zip">Download</a></td>
</tr>
<tr>
<td>J</td>
<td><a href="images/metamodule-J.png"><img src="images/metamodule-J_crop_resize.jpg" alt="Meta-module J" style="max-width:100%;"></a></td>
<td>1,078</td>
<td>62,768</td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-J_filterlevel-any.zip">Download</a></td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-J_filterlevel-any_tfOnly.zip">Download</a></td>
</tr>
<tr>
<td>K</td>
<td><a href="images/metamodule-K.png"><img src="images/metamodule-K_crop_resize.jpg" alt="Meta-module K" style="max-width:100%;"></a></td>
<td>42</td>
<td>145</td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-K_filterlevel-any.zip">Download</a></td>
<td><a href="//github.com/markmagnuson/BetaCell-GCN/raw/master/cyjs/metamodule-K_filterlevel-any_tfOnly.zip">Download</a></td>
</tr>
</tbody>
</table>
<hr>
<small>
<h5>Legend</h5>
<ol>
<li>A node represents a gene</li>
<li>An edge represents a connection between two nodes and the number of edges shown is representative of edges with correlations of greater than 0.5</li>
</ol>
</small>
<h2>FAQ</h2>
<h4>Where can I get Cytoscape?</h4>
<p>You can download it <a href="http://www.cytoscape.org/">here</a>.</p>
<h4>How do I load network files in Cytoscape?</h4>
<p>In order to load a network from a local file you can select File → Import → Network → File... Choose the correct file in the file chooser dialog and press Open. After you choose a network file, another dialog will pop up. Here, you can choose either to create a new network collection for the new network, or load the new network into an existing network collection. When you choose the latter, make sure to choose the right mapping column to map the new network to the existing network collection.</p>
<h3>Contact</h3>
<p>If you have questions, please contact the corresponding author of the manuscript or post an issue in the GitHub issue tracker for this repository.</p>
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