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<%@ page language="java" contentType="text/html; charset=US-ASCII"
pageEncoding="US-ASCII"%>
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<%@ page import="edu.mssm.pharm.maayanlab.X2K.web.*"%>
<%@ page import="edu.mssm.pharm.maayanlab.X2K.enrichment.*"%>
<%@ page import="edu.mssm.pharm.maayanlab.ChEA.*"%>
<%@ page import="edu.mssm.pharm.maayanlab.Genes2Networks.*"%>
<%@ page import="edu.mssm.pharm.maayanlab.KEA.*"%>
<html>
<head>
<title>X2K Web</title>
<!-- JavaScript imports -->
<script src="js/jquery-3.0.0.min.js"></script>
<script
src="https://cdnjs.cloudflare.com/ajax/libs/Chart.js/2.1.6/Chart.bundle.min.js"></script>
<script type="text/javascript" src="js/index.js"></script>
<script type="text/javascript"
src="//s7.addthis.com/js/300/addthis_widget.js#pubid=ra-578e939ffe83e029"></script>
<!-- Load favicon -->
<link rel="shortcut icon" href="favicon.ico" type="image/x-icon" />
<!-- CSS -->
<link href="https://fonts.googleapis.com/css?family=Lato:300,400,700"
rel="stylesheet">
<link rel="stylesheet" href="css/main.css">
<link rel="stylesheet" href="css/api.css">
<script>
(function(i, s, o, g, r, a, m) {
i['GoogleAnalyticsObject'] = r;
i[r] = i[r] || function() {
(i[r].q = i[r].q || []).push(arguments)
}, i[r].l = 1 * new Date();
a = s.createElement(o), m = s.getElementsByTagName(o)[0];
a.async = 1;
a.src = g;
m.parentNode.insertBefore(a, m)
})(window, document, 'script',
'https://www.google-analytics.com/analytics.js', 'ga');
ga('create', 'UA-6277639-28', 'auto');
ga('send', 'pageview');
</script>
</head>
<body>
<div id="page">
<%@ include file="templates/frame/header.html"%>
<div id="content">
<div>
<ul id="menu">
<li><a href="#x2k" class="setting tab-link">X2K</a></li>
<li><a href="#downloads" class="information tab-link">Downloads</a></li>
<li><a href="#help" class="information tab-link">Help</a></li>
</ul>
</div>
<div id="top_bar">
<div class="clear"></div>
</div>
<!-- The form that occupies most of the page, storing all settings -->
<form id="settings_form" action="network" method="POST"
enctype="multipart/form-data">
<!-- Tab content -->
<div id="x2k" class="tab-content">
<div id="input-fields" class="section">
<div id="text-input">
<h4 class="section-label">Enter a list of human or mouse Entrez gene symbols here:</h4>
<textarea rows="12" name="text-genes" id="text-genes"></textarea>
<table id="run-buttons-container">
<tbody>
<tr>
<td><button type="button" id="example-gene-list">Example</button>
</td>
<!-- <td><input id="file" type="file" name="file" class="inputfile"/><label for="file" id="download-label">Input genes as file</label>
</td>
--><td>
<div id="run-buttons">
<button type="submit" id="results_submit">Submit</button>
</div>
</td>
</tr>
</tbody>
</table>
</div>
</div>
<button class="accordion" id="acc_settings"></button>
<div id="settings" class="panel">
<button class="accordion" id="acc_x2k"></button>
<div id="x2k-settings" class="panel">
Minimum number of proteins in subnetwork: <input type="text"
name="${X2K.MINIMUM_NETWORK_SIZE}" size="3" value="50"></br>
Number of results: <input type="text"
name="number_of_results" size="3" value="10">
</div>
<button class="accordion" id="acc_chea"></button>
<div id="chea-settings" class="panel">
Sort by: <input type="radio" name="${ChEA.SORT_BY}"
value="${ChEA.PVALUE}"> p-value <input type="radio"
name="${ChEA.SORT_BY}" value="${ChEA.RANK}"> rank <input
type="radio" name="${ChEA.SORT_BY}"
value="${ChEA.COMBINED_SCORE}" checked="checked">
combined score<br> <br> Background organism: <input
type="radio" name="${ChEA.INCLUDED_ORGANISMS}"
value="${ChEA.MOUSE_ONLY}"> mouse <input type="radio"
name="${ChEA.INCLUDED_ORGANISMS}" value="${ChEA.HUMAN_ONLY}">
human <input type="radio" name="${ChEA.INCLUDED_ORGANISMS}"
value="${ChEA.BOTH}" checked="checked"> both<br> <br>
Transcription factor database:<br> <input type="radio"
name="${ChEA.BACKGROUND_DATABASE}" value="${ChEA.CHEA_2015}"
checked="checked"> ChEA 2015 <br> <input
type="radio" name="${ChEA.BACKGROUND_DATABASE}"
value="${ChEA.ENCODE_2015}"> ENCODE 2015 <br> <input
type="radio" name="${ChEA.BACKGROUND_DATABASE}"
value="${ChEA.CONSENSUS}"> ChEA & ENCODE Consensus <br>
<input type="radio" name="${ChEA.BACKGROUND_DATABASE}"
value="${ChEA.TRANS_JASP}"> Transfac & Jaspar<br>
</div>
<button class="accordion" id="acc_g2n"></button>
<div id="g2n-settings" class="panel">
<input type="text" name="${Genes2Networks.PATH_LENGTH}" size="5"
value="2"> Path Length<br> <input type="text"
name="${Genes2Networks.MINIMUM_NUMBER_OF_ARTICLES}" size="5"
value="2"> Minimum Number of Articles<br> <input
type="text" name="${Genes2Networks.MAXIMUM_NUMBER_OF_EDGES}"
size="5" value="200"> Maximum Number of Edges per Node<br>
<input type="text"
name="${Genes2Networks.MAXIMUM_NUMBER_OF_INTERACTIONS}" size="5"
value="100"> Maximum Number of Interactions per Article<br>
<!-- experiment -i've been told this works even though its shady -->
<br> Use the following PPI Networks: <br>
<input type="checkbox" name="${Genes2Networks.ENABLE_BIOCARTA}" value="true" checked>
Biocarta
<input type="hidden" name="${Genes2Networks.ENABLE_BIOCARTA}" value="false">
<input type="checkbox" name="${Genes2Networks.ENABLE_BIOGRID}" value="true" checked>
BioGRID
<input type="hidden" name="${Genes2Networks.ENABLE_BIOGRID}" value="false">
<input type="checkbox" name="${Genes2Networks.ENABLE_BIOPLEX}" value="true" checked>
BioPlex
<input type="hidden" name="${Genes2Networks.ENABLE_BIOPLEX}" value="false">
<input type="checkbox" name="${Genes2Networks.ENABLE_DIP}" value="true" checked>
DIP
<input type="hidden" name="${Genes2Networks.ENABLE_DIP}" value="false">
<input type="checkbox" name="${Genes2Networks.ENABLE_HUMAP}" value="true" checked>
huMAP
<input type="hidden" name="${Genes2Networks.ENABLE_HUMAP}" value="false">
<input type="checkbox" name="${Genes2Networks.ENABLE_INNATEDB}" value="true" checked>
InnateDB
<input type="hidden" name="${Genes2Networks.ENABLE_INNATEDB}" value="false">
<br>
<input type="checkbox" name="${Genes2Networks.ENABLE_INTACT}" value="true" checked>
IntAct
<input type="hidden" name="${Genes2Networks.ENABLE_INTACT}" value="false">
<input type="checkbox" name="${Genes2Networks.ENABLE_KEGG}" value="true" checked>
KEGG
<input type="hidden" name="${Genes2Networks.ENABLE_KEGG}" value="false">
<input type="checkbox" name="${Genes2Networks.ENABLE_MINT}" value="true" checked>
MINT
<input type="hidden" name="${Genes2Networks.ENABLE_MINT}" value="false">
<input type="checkbox" name="${Genes2Networks.ENABLE_PPID}" value="true" checked>
ppid
<input type="hidden" name="${Genes2Networks.ENABLE_PPID}" value="false">
<input type="checkbox" name="${Genes2Networks.ENABLE_SNAVI}" value="true" checked>
SNAVI
<input type="hidden" name="${Genes2Networks.ENABLE_SNAVI}" value="false">
</div>
<button class="accordion" id="acc_kea"></button>
<div id="kea-settings" class="panel">
<br> Sort by: <br>
<input type="radio" name="${KEA.SORT_BY}" value="${KEA.PVALUE}"
checked="checked"> p-value <input type="radio"
name="${KEA.SORT_BY}" value="${KEA.RANK}"> rank <input
type="radio" name="${KEA.SORT_BY}" value="${KEA.COMBINED_SCORE}"
checked="checked"> combined score<br>
</div>
</div>
</div>
<div id="downloads" class="tab-content">
<h3>Command-line versions</h3>
You can download command line standalone versions of the X2K tools in JAR format.
Command near each download link suggests usage:
<p>
<a
href=http://www.maayanlab.net/X2K/download/install_X2K.jar>X2K
with source code (61.3 MB)</a>
<code>java -jar X2K.jar genelist output.xml</code>
</p>
<p>
<a
href=http://www.maayanlab.net/X2K/download/X2K-1.5-SNAPSHOT-jar-with-dependencies.jar>X2K
only binary (28.9 MB)</a>
<code>java -jar X2K.jar genelist output.xml</code>
</p>
<p>
<a
href=http://www.maayanlab.net/X2K/download/ChEA-1.5-SNAPSHOT-jar-with-dependencies.jar>ChEA
(8.1 MB)</a>
<code>java -jar ChEA.jar [background] genelist output.csv</code>
</p>
<p>
<a
href=http://www.maayanlab.net/X2K/download/G2N-1.5-SNAPSHOT-jar-with-dependencies.jar>G2N
(3.6 MB)</a>
<code>java -jar G2N.jar input output.sig
[backgroundSigFiles...]</code>
</p>
<p>
<a
href=http://www.maayanlab.net/X2K/download/KEA-1.5-SNAPSHOT-jar-with-dependencies.jar>KEA
(188 KB)</a>
<code>java -jar KEA.jar [background] genelist output.csv</code>
</p>
<p>
<a
href=http://www.maayanlab.net/X2K/download/List2Networks-1.0-SNAPSHOT-jar-with-dependencies.jar>L2N
(2 MB)</a>
<code>java -jar L2N.jar gene_list [background_file...]
output.xml</code>
</p>
<h3>Datasets</h3>
<dl>
<dt>Transcriptional Regulation</dt>
<p>
<a href="datasets/ChEA2015.zip"> ChEA 2015 </a>
</p>
<p>
<a href="datasets/ENCODE2015.zip"> ENCODE 2015 </a>
</p>
<p>
<a href="datasets/Consensus.zip"> ChEA & ENCODE Consensus </a>
</p>
<p>
<a href="datasets/TransfacAndJaspar.zip"> TRANSFAC & JASPAR </a>
</p>
</dl>
<dl>
<dt>Protein-Protein Interaction</dt>
<p>
<a href="datasets/Biocarta.sig"> Biocarta </a>
</p>
<p>
<a href="datasets/BioGrid.sig"> BioGrid </a>
</p>
<p>
<a href="datasets/BioPlex.sig"> BioPlex </a>
</p>
<p>
<a href="datasets/DIP.sig"> DIP </a>
</p>
<p>
<a href="datasets/huMAP.sig"> huMAP </a>
</p>
<p>
<a href="datasets/innateDB.sig"> innateDB </a>
</p>
<p>
<a href="datasets/IntAct.sig"> IntAct </a>
</p>
<p>
<a href="datasets/KEGG.sig"> KEGG </a>
</p>
<p>
<a href="datasets/MINT.sig"> MINT </a>
</p>
<p>
<a href="datasets/ppid.sig"> ppid </a>
</p>
<p>
<a href="datasets/SNAVI.sig"> SNAVI </a>
</p>
</dl>
<dl>
<dt>Kinome Regulation</dt>
<p>
<a href="datasets/KEA.zip"> KEA 2015 </a>
</p>
</dl>
</div>
<div id="help" class="tab-content">
<h3>About</h3>
<div id="manual">
<p>
X2K Web is an online tool used to infer upstream regulatory
networks from differentially expressed genes. Combining the <a
href="http://amp.pharm.mssm.edu/Enrichr">ChEA</a>, Genes2Networks,
and <a href="http://www.maayanlab.net/KEA2/">KEA</a> apps
together, X2K Web produces inferred networks of transcription
factors, proteins, and kinases which take part in the upstream
regulation of the inputted gene list. X2K web also allows users to
analyze their differentially expressed gene lists using ChEA, G2N,
and KEA individually. To read more about the concept of X2K, you
can read about it <a href="http://www.maayanlab.net/X2K/">here</a>.
</p>
</div>
<h3>Instructional Video</h3>
<div id="about">
<iframe width="560" height="315" src="https://www.youtube.com/embed/ipchvqQhdpc" frameborder="0" allowfullscreen></iframe>
</div>
<h3>API</h3>
<div id="api">
<%@ include file="templates/help/api.html"%>
</div>
<!-- <h3>Statistics</h3>
<div id="statistics">
<div id="ChEA_stats">
<h3 class="stat_category">ChEA Datasets</h3>
<p>Histograms for each of the ChEA datasets depicting the
number of nodes with certain numbers of interactions per node in
the Transcription Factor-Transcription Factor network.</p>
</div>
<div class="clear"></div>
<div id="G2N_stats">
<h3 class="stat_category">G2N Datasets</h3>
<p>Histograms for each of the Genes2Networks datasets
depicting the number of nodes with certain numbers of
interactions per node in the Protein-Protein Interaction
Netowork.</p>
</div>
<div class="clear"></div>
<div id="KEA_stats">
<h3 class="stat_category">KEA Datasets</h3>
<p>Histograms for each of the KEA datasets depicting the
number of nodes with certain numbers of interactions per node in
the Kinase-Kinase network.</p>
</div>
<div class="clear"></div>
</div>
<div id="affiliations">
<h3>Affiliations</h3>
<div id="affiliations">
<ul id="affiliations_list">
<li><a
href="http://icahn.mssm.edu/research/labs/maayan-laboratory"
target="_blank">The Ma'ayan Lab</a></li>
<li><a href="http://www.lincs-dcic.org/" target="_blank">BD2K-LINCS
Data Coordination and Integration Center (DCIC)</a></li>
<li><a href="http://www.lincsproject.org/">NIH LINCS
program</a></li>
<li><a href="http://bd2k.nih.gov/" target="_blank">NIH
Big Data to Knowledge (BD2K)</a></li>
<li><a href="https://commonfund.nih.gov/idg/index"
target="_blank">NIH Illuminating the Druggable Genome (IDG)
Program</a></li>
<li><a href="http://icahn.mssm.edu/" target="_blank">Icahn
School of Medicine at Mount Sinai</a></li>
</ul>
</div>
</div>
-->
</div>
</form>
<div class="clear"></div>
</div>
<%@ include file="templates/frame/footer.html"%>
</div>
</body>
</html>