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<li><a href="#expr">Expression data</a></li>
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<li><a href="#GOtreeBP">The BP GO tree</a></li>
<li><a href="#GOtreeCC">The CC GO tree</a></li>
<li><a href="#GOtreeMF">The MF GO tree</a></li>
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<li><a href="#GOBP">GO BP enrichment</a></li>
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<li><a href="#GOMF">GO MF enrichment</a></li>
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<li><a href="#genes">Genes</a></li>
<li><a href="#conds">Conditions</a></li>
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<h2 id="expr"><span class="hideshow">
<span id="section.5.1" style="position:absolute;top:0;right:0;">
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Expression data</h2>

<div id="help.5" style="background:#eaeaea;display:none;visibility:hidden;width:100%;">
<div style="width:800px;margin:10px 10px 10px 10px;">
<h3>HELP</h3>
<p>
The image plot shows the color-coded level of gene expression, for the
genes and conditions in a  given transcription module. The genes are on
the horizontal, the conditions on the vertical axis.
</p>
<p>
The genes are ordered according to their ISA gene scores, similarly
the conditions are ordered according to their condition scores. The
score of a gene means the &laquo;degree of inclusion&raquo; in 
the module: a high score gene is essential in the module.
</p>

<p>
Condition scores can also be negative, that means that the genes of
the module are all down-regulated in the condition. Here the absolute
value of the score gives the &laquo;degree of inclusion&raquo;.
</p>

<p>
The plots above and beside the expression matrix show the gene scores
and condition scores, respectively.
</p>

<p>
Note that the plot is interactive, you can see the name of the gene
and condition under the mouse cursor.
</p>

<p>
The expression matrix was normalized to have mean zero and standard
deviation one for every gene separately across all conditions
(i.e. not just for the conditions in the module).
</p>

<p class="note">
&mdash; Click on the <i>Help</i> button again to close this help window.
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<label for="exp.x">Gene: </label><input id="exp.x" value=""
  readonly="readonly" style="width:800px; border: none;"/><br/>
<label for="exp.y">Condition: </label><input id="exp.y" value=""
  readonly="readonly" style="width:800px; border: none;"/>
</p>
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     style="position:absolute;width:1px;height:<!--expy-->px;background: yellow;left:101px;display:none;z-index:11;">
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<img src="expression-<!--no-->.png" alt="Expression data for module #<!--no-->" 
     onmousemove="writeCoords(event);" id="expimage" 
     style="position:relative;left:0px;top:10px;"/>
</div>
<div style="clear:both; height:10px;"></div>
<p class="note"><img src="expcolbar-<!--no-->.png" alt="color bar"/><br/>
Under-expression is coded with <span style="color:green;">green</span>, 
over-expression with <span style="color:red;">red</span> color.</p>
</div>

<div style="clear:both;"></div>
</div>

<h2 id="GOtreeBP"><span class="hideshow">
<span id="section.7.1" style="position:absolute;top:0;right:0;">
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The GO tree &mdash; Biological processes</h2>

<div id="help.7" style="background:#eaeaea;display:none;visibility:hidden;width:100%;">
<div style="width:800px;margin:10px 10px 10px 10px;">
<h3>HELP</h3>
<p>
This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for <b>biological processes</b>. 
</p>

<p>
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
&laquo;is a&raquo; (cyan) and &laquo;part of&raquo; relationships.
</p>

<p>
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
</p>

<p>
Note that the same GO category might show up on the graph many
times. This is because the GO was &laquo;straightened&raquo; for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers 
</p>

<p>
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
</p>

<p>
If you cannot see a graph here at all, that means that there were no 
significantly enriched GO categories, at the 0.05 level.
</p>

<p class="note">
&mdash; Click on the <i>Help</i> button again to close this help window.
</p>
</div>
<div style="clear:both;height:2px;background:url(images/headerbg.png) repeat-x;"></div>
</div>

<div id="section.7">

<p class="note"><img src="images/colbar.png" alt="color bar" /></p>
<dl class="map" id="mapbp">
<!-- GOtreeBP -->
<!-- /GOtreeBP -->
</dl>
</div>

<h2 id="GOtreeCC"><span class="hideshow">
<span id="section.10.1" style="position:absolute;top:0;right:0;">
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The GO tree &mdash; Cellular Components</h2>

<div id="help.10" style="background:#eaeaea;display:none;visibility:hidden;width:100%;">
<div style="width:800px;margin:10px 10px 10px 10px;">
<h3>HELP</h3>
<p>
This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for <b>cellular components</b>. 
</p>

<p>
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
&laquo;is a&raquo; (cyan) and &laquo;part of&raquo; relationships.
</p>

<p>
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
</p>

<p>
Note that the same GO category might show up on the graph many
times. This is because the GO was &laquo;straightened&raquo; for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers 
</p>

<p>
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
</p>

<p>
If you cannot see a graph here at all, that means that there were no 
significantly enriched GO categories, at the 0.05 level.
</p>

<p class="note">
&mdash; Click on the <i>Help</i> button again to close this help window.
</p>
</div>
<div style="clear:both;height:2px;background:url(images/headerbg.png) repeat-x;"></div>
</div>

<div id="section.10">

<p class="note"><img src="images/colbar.png" alt="color bar"/></p>
<dl class="map" id="mapcc">
<!-- GOtreeCC -->
<!-- /GOtreeCC -->
</dl>
</div>

<h2 id="GOtreeMF"><span class="hideshow">
<span id="section.11.1" style="position:absolute;top:0;right:0;">
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The GO tree &mdash; Molecular Function</h2>

<div id="help.11" style="background:#eaeaea;display:none;visibility:hidden;width:100%;">
<div style="width:800px;margin:10px 10px 10px 10px;">
<h3>HELP</h3>
<p>
This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for <b>molecular function</b>. 
</p>

<p>
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
&laquo;is a&raquo; (cyan) and &laquo;part of&raquo; relationships.
</p>

<p>
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
</p>

<p>
Note that the same GO category might show up on the graph many
times. This is because the GO was &laquo;straightened&raquo; for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers 
</p>

<p>
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
</p>

<p>
If you cannot see a graph here at all, that means that there were no 
significantly enriched GO categories, at the 0.05 level.
</p>

<p class="note">
&mdash; Click on the <i>Help</i> button again to close this help window.
</p>
</div>
<div style="clear:both;height:2px;background:url(images/headerbg.png) repeat-x;"></div>
</div>

<div id="section.11">

<p class="note"><img src="images/colbar.png" alt="color bar"/></p>
<dl class="map" id="mapmf">
<!-- GOtreeMF -->
<!-- /GOtreeMF -->
</dl>
</div>

<h2 id="GOBP"><span class="hideshow">
<span id="section.1.1" style="position:absolute;top:0;right:0;display:none;">
<a href="#" onclick="togglestuff2('help.1'); return false;">Help</a> |
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<span id="section.1.2" style="position:absolute;top:0;right:0;">
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</span>
GO BP test for over-representation</h2>

<div id="help.1" style="background:#eaeaea;display:none;visibility:hidden;width:100%;">
<div style="width:800px;margin:10px 10px 10px 10px;">
<h3>HELP</h3>
<p>
List of all enriched GO categories (biological processes), at the 0.05
p-value level.
</p>

<p>
The columns: 
<ul><li><b>ExpCount</b> is the expected count of genes in the
module annotated with the given GO term, just by chance. </li>
<li><b>Count</b>
is the number of genes in the module annotated with the given GO
term. </li>
<li><b>Size</b> is the total number of genes (in our universe)
annotated with the GO term.</li>
</ul>
</p>

<p>
Clicking on <b>Count</b> shows the genes that drive the
enrichment. You can also click on the individual numbers in
the <b>Count</b> column, to show the driving genes for that individual
GO category.
</p>

<p>
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
</p>

<p class="note">
&mdash; Click on the <i>Help</i> button again to close this help window.
</p>
</div>
<div style="clear:both;height:2px;background:url(images/headerbg.png) repeat-x;"></div>
</div>

<div id="section.1" style="display:none;visibility:hidden;">

<table style="border:0px;">
<!-- tableGOBP -->
<!-- /tableGOBP -->
</table>
</div>

<h2 id="GOCC"><span class="hideshow">
<span id="section.2.1" style="position:absolute;top:0;right:0;display:none;">
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</span>
<span id="section.2.2" style="position:absolute;top:0;right:0;">
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</span>
GO CC test for over-representation</h2>

<div id="help.2" style="background:#eaeaea;display:none;visibility:hidden;width:100%;">
<div style="width:800px;margin:10px 10px 10px 10px;">
<h3>HELP</h3>
<p>
List of all enriched GO categories (cellular components), at the 0.05
p-value level.
</p>

<p>
The columns: 
<ul><li><b>ExpCount</b> is the expected count of genes in the
module annotated with the given GO term, just by chance. </li>
<li><b>Count</b>
is the number of genes in the module annotated with the given GO
term. </li>
<li><b>Size</b> is the total number of genes (in our universe)
annotated with the GO term.</li>
</ul>
</p>

<p>
Clicking on <b>Count</b> shows the genes that drive the
enrichment. You can also click on the individual numbers in
the <b>Count</b> column, to show the driving genes for that individual
GO category.
</p>

<p>
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
</p>

<p class="note">
&mdash; Click on the <i>Help</i> button again to close this help window.
</p>
</div>
<div style="clear:both;height:2px;background:url(images/headerbg.png) repeat-x;"></div>
</div>

<div id="section.2" style="display:none;visibility:hidden;">
<table border="0">
<!-- tableGOCC -->
<!-- /tableGOCC -->
</table>
</div>

<h2 id="GOMF"><span class="hideshow">
<span id="section.3.1" style="position:absolute;top:0;right:0;display:none;">
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<span id="section.3.2" style="position:absolute;top:0;right:0;">
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</span>
GO MF test for over-representation</h2>

<div id="help.3" style="background:#eaeaea;display:none;visibility:hidden;width:100%;">
<div style="width:800px;margin:10px 10px 10px 10px;">
<h3>HELP</h3>
<p>
List of all enriched GO categories (molecular function), at the 0.05
p-value level.
</p>

<p>
The columns: 
<ul><li><b>ExpCount</b> is the expected count of genes in the
module annotated with the given GO term, just by chance. </li>
<li><b>Count</b>
is the number of genes in the module annotated with the given GO
term. </li>
<li><b>Size</b> is the total number of genes (in our universe)
annotated with the GO term.</li>
</ul>
</p>

<p>
Clicking on <b>Count</b> shows the genes that drive the
enrichment. You can also click on the individual numbers in
the <b>Count</b> column, to show the driving genes for that individual
GO category.
</p>

<p>
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
</p>

<p class="note">
&mdash; Click on the <i>Help</i> button again to close this help window.
</p>
</div>
<div style="clear:both;height:2px;background:url(images/headerbg.png) repeat-x;"></div>
</div>

<div id="section.3" style="display:none;visibility:hidden;">
<table border="0">
<!-- tableGOMF -->
<!-- /tableGOMF -->  
</table>
</div>

<h2 id="KEGG"><span class="hideshow">
<span id="section.4.1" style="position:absolute;top:0;right:0;">
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</span>
KEGG Pathway test for over-representation</h2>

<div id="help.4" style="background:#eaeaea;display:none;visibility:hidden;width:100%;">
<div style="width:800px;margin:10px 10px 10px 10px;">
<h3>HELP</h3>
<p>
List of all enriched KEGG pathways, at the 0.05
p-value level.
</p>

<p>
The columns: 
<ul><li><b>ExpCount</b> is the expected count of genes in the
module annotated with the given KEGG pathway, just by chance. </li>
<li><b>Count</b>
is the number of genes in the module annotated with the given KEGG
pathway. </li>
<li><b>Size</b> is the total number of genes (in our universe)
annotated with the KEGG pathway.</li>
</ul>
</p>

<p>
Clicking on <b>Count</b> shows the genes that drive the
enrichment. You can also click on the individual numbers in
the <b>Count</b> column, to show the driving genes for that individual
KEGG pathway.
</p>

<p>
Clicking on the KEGG identifiers takes you to the KEGG web site.
</p>

<p class="note">
&mdash; Click on the <i>Help</i> button again to close this help window.
</p>
</div>
<div style="clear:both;height:2px;background:url(images/headerbg.png) repeat-x;"></div>
</div>

<div id="section.4">
<table border="0">
<!-- tableKEGG -->
<!-- /tableKEGG -->
</table>
</div>

<h2 id="miRNA"><span class="hideshow">
<span id="section.12.1" style="position:absolute;top:0;right:0;">
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</span>
<span id="section.12.2" style="position:absolute;top:0;right:0;display:none;">
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</span>
</span>
miRNA test for over-representation</h2>

<div id="help.12" style="background:#eaeaea;display:none;visibility:hidden;width:100%;">
<div style="width:800px;margin:10px 10px 10px 10px;">
<h3>HELP</h3>
<p>
List of all enriched miRNA families, at the 0.05
p-value level.
</p>

<p>
The columns: 
<ul><li><b>ExpCount</b> is the expected count of genes in the
module regulated by the given miRNA family, just by chance. </li>
<li><b>Count</b>
is the number of genes in the module regulated by the given miRNA
family.</li>
<li><b>Size</b> is the total number of genes (in our universe)
regulated with the given miRNA family.</li>
</ul>
</p>

<p>
Clicking on <b>Count</b> shows the genes that drive the
enrichment. You can also click on the individual numbers in
the <b>Count</b> column, to show the driving genes for that individual
miRNA family.
</p>

<p>
The miRNA regulation data was taken from the <a
href="http://targetscan.org">TargetScan</a> database.
(Only the conserved sites were used for the current analysis.)
Clicking on the miRNA names takes you to the TargetScan web site.
</p>

<p class="note">
&mdash; Click on the <i>Help</i> button again to close this help window.
</p>
</div>
<div style="clear:both;height:2px;background:url(images/headerbg.png) repeat-x;"></div>
</div>

<div id="section.12">
<table border="0">
<!-- tablemiRNA -->
<!-- /tablemiRNA -->
</table>
</div>

<h2 id="CHR"><span class="hideshow">
<span id="section.14.1" style="position:absolute;top:0;right:0;">
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</span>
Chromosome test for over-representation</h2>

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<h3>HELP</h3>
<p>
List of all enriched Chromosomes, at the 0.05
p-value level.
</p>

<p>
The columns: 
<ul><li><b>ExpCount</b> is the expected number of genes in the
module on the given chromosome, just by chance. </li>
<li><b>Count</b>
is the number of genes in the module on the given chromosome.</li>
<li><b>Size</b> is the total number of genes (in our universe)
on the given chromosome.</li>
</ul>
</p>

<p>
Clicking on <b>Count</b> shows the genes that drive the
enrichment. You can also click on the individual numbers in
the <b>Count</b> column, to show the driving genes for that individual
chromosome.
</p>

<p class="note">
&mdash; Click on the <i>Help</i> button again to close this help window.
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</table>
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<h2 id="genes"><span class="hideshow">
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Genes</h2>

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<h3>HELP</h3>
<p>
A list of all genes in the current module, in alphabetical order. The
size of the text corresponds to the gene scores. 
</p>

<p>
Note that some gene symbols may show up more than once, if many
probes match the same Entrez gene.
</p>

<p>
Genes with no Entrez mapping are given separately, with their
Affymetrics probe ID.
</p>

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<h3>Entrez genes</h3>
<p>
<!-- genecloud -->
<!-- /genecloud -->
</p>
<h3>Non-Entrez genes</h3>
<!-- genecloud-noname -->
<!-- /genecloud-noname -->
</div>

<h2 id="conds"><span class="hideshow">
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Conditions</h2>

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<h3>HELP</h3>
<p>
Conditions in the module, given in the same order as on the expression
plot above. Red color means over-expression, green under-expression in
the given condition.
</p>

<p>
The barplot below shows the condition (sample) scores. A separate bar
is shown for each sample, its height is the corresponding score of the
sample in the module. The red and green numbers on the bars are the
sample scores expressed in percents, i.e. 100% is 1.0.
</p>

<p>
The red and green lines show the module thresholds, samples above
the red line and below the green line are included in the module.
</p>

<p>
The different experiments that were part of the study, are separated
by dashed vertical lines. 
</p>

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&mdash; Click on the <i>Help</i> button again to close this help window.
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   &copy; 2008-2010 Computational Biology Group, Department of Medical Genetics,
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