MSigDB v4.0 Release Notes

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<a href="http://www.broadinstitute.org/gsea/">GSEA Home</a> |  <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a>  | <a href="http://www.broadinstitute.org/gsea/msigdb/">Molecular  Signatures Database</a> | <a href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page">Documentation</a> | <a href="http://www.broadinstitute.org/gsea/contact.jsp">Contact</a>  <br />
<a href="http://www.broadinstitute.org/gsea/">GSEA Home</a> |  <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a>  | <a href="http://www.broadinstitute.org/gsea/msigdb/">Molecular  Signatures Database</a> | <a href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page">Documentation</a> | <a href="http://www.broadinstitute.org/gsea/contact.jsp">Contact</a>  <br />
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<h2> Gene set name changes</h2>
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<p>There were no changes to gene set names that were present in v3.1 MSigDB and which remained in v4.0 MSigDB.</p>
<h2>New collection C7: Immunologic Signatures</h2>
<h2>New collection C7: Immunologic Signatures</h2>
<p><strong>C7: Immunologic Signatures (ImmuneSig)</strong> is a <strong>new collection</strong> of 1910 sets. These gene sets represent cell types, states, and perturbations within the immune system. The signatures were generated by manual curation of published studies in human and mouse immunology.</p>
<p><strong>C7: Immunologic Signatures (ImmuneSig)</strong> is a <strong>new collection</strong> of 1910 sets. These gene sets represent cell types, states, and perturbations within the immune system. The signatures were generated by manual curation of published studies in human and mouse immunology.</p>
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<p>This resource was generated as part of the <strong>[http://www.immuneprofiling.org Human Immunology Project Consortium (HIPC)] </strong>.</p>
<p>This resource was generated as part of the <strong>[http://www.immuneprofiling.org Human Immunology Project Consortium (HIPC)] </strong>.</p>
<h2>Updates to C2 collection</h2>
<h2>Updates to C2 collection</h2>
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<p> We have removed <strong>all</strong> 132 gene sets which originated from the <strong>
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[http://mips.helmholtz-muenchen.de/genre/proj/corum Munich Information Center for Protein Sequences (CORUM MIPS)]</strong> database because they no longer allow redistribution of this information. Previously, these sets were part of Canonical Pathways (CP) in the C2 collection.</p>
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<p><strong>Four (4) new gene sets</strong> curated from papers were added to the <strong>C2:CGP</strong> (Chemical and Genetic Perturbations) sub-collection.</p>
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<h2>Updates to C4: Cancer Modules</h2>
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<p>We have fixed an error in the external link URLs for all 431 sets in the <strong>C4:CM</strong> (Cancer Modules) sub-collection.</p>
<h2> Viewing previous versions of MSigDB</h2>
<h2> Viewing previous versions of MSigDB</h2>
<p>Files from previous versions of MSigDB (v3.1, v3.0, v2.5, v2.1 and v1.0) are archived and available at [http://www.broadinstitute.org/gsea/downloads.jsp Downloads]  page. You can view them through the MSigDB Browser tool in the GSEA desktop application.</p>
<p>Files from previous versions of MSigDB (v3.1, v3.0, v2.5, v2.1 and v1.0) are archived and available at [http://www.broadinstitute.org/gsea/downloads.jsp Downloads]  page. You can view them through the MSigDB Browser tool in the GSEA desktop application.</p>

Revision as of 18:44, 5 June 2013

<a href="http://www.broadinstitute.org/gsea/">GSEA Home</a> | <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> | <a href="http://www.broadinstitute.org/gsea/msigdb/">Molecular Signatures Database</a> | <a href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page">Documentation</a> | <a href="http://www.broadinstitute.org/gsea/contact.jsp">Contact</a>

Contents

Gene set name changes

There were no changes to gene set names that were present in v3.1 MSigDB and which remained in v4.0 MSigDB.

New collection C7: Immunologic Signatures

C7: Immunologic Signatures (ImmuneSig) is a new collection of 1910 sets. These gene sets represent cell types, states, and perturbations within the immune system. The signatures were generated by manual curation of published studies in human and mouse immunology.

We first captured relevant microarray datasets published in the immunology literature that have raw data deposited to Gene Expression Omnibus (GEO). Next, for each published study, the relevant comparisons were identified (e.g. WT vs. KO; pre- vs. post-treatment etc.) and brief, biologically meaningful descriptions were created. Then we processed and normalized every data set the same way to identify gene sets, which correspond to the top or bottom genes (FDR < 0.25 or maximum of 200 genes) ranked by mutual information for each assigned comparison.

This resource was generated as part of the Human Immunology Project Consortium (HIPC) .

Updates to C2 collection

We have removed all 132 gene sets which originated from the Munich Information Center for Protein Sequences (CORUM MIPS) database because they no longer allow redistribution of this information. Previously, these sets were part of Canonical Pathways (CP) in the C2 collection.

Four (4) new gene sets curated from papers were added to the C2:CGP (Chemical and Genetic Perturbations) sub-collection.

Updates to C4: Cancer Modules

We have fixed an error in the external link URLs for all 431 sets in the C4:CM (Cancer Modules) sub-collection.

Viewing previous versions of MSigDB

Files from previous versions of MSigDB (v3.1, v3.0, v2.5, v2.1 and v1.0) are archived and available at Downloads page. You can view them through the MSigDB Browser tool in the GSEA desktop application.

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