MSigDB v5.2 Release Notes

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<p>We added 4 gene sets (submitted by Dr. Eppert, MgGill University) and redefined the gene set [http://software.broadinstitute.org/gsea/msigdb/cards/MCLACHLAN_DENTAL_CARIES_DN.html MCLACHLAN_DENTAL_CARIES_DN]</p>
<p>We added 4 gene sets (submitted by Dr. Eppert, MgGill University) and redefined the gene set [http://software.broadinstitute.org/gsea/msigdb/cards/MCLACHLAN_DENTAL_CARIES_DN.html MCLACHLAN_DENTAL_CARIES_DN]</p>
<h2>Overhaul of C5 - gene ontology</h2>
<h2>Overhaul of C5 - gene ontology</h2>
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<p>We deprecated the entir</p>
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<p> Gene sets in this collection are derived from the controlled vocabulary of the Gene Ontology (GO) project: The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology ([http://www.geneontology.org Nature Genet 2000]). The gene sets are named by GO term and contain genes annotated by that term. We have deprecated the entire collection and define new gene sets using more recent GO term annotations.</p>
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<p> Gene sets in this new collection are derived from the controlled vocabulary of the Gene Ontology (GO) project: The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology ([http://www.geneontology.org Nature Genet 2000]). The gene sets are named by GO term and contain genes annotated by that term.</p>
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<p>This collection is divided into three subcollections:</p>
<p>This collection is divided into three subcollections:</p>
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     <li><strong>BP</strong>: GO Biological process (+4653 gene sets). Gene sets derived from the Biological Process Ontology.</li>
     <li><strong>BP</strong>: GO Biological process (+4653 gene sets). Gene sets derived from the Biological Process Ontology.</li>
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<p>Among the deprecated C5 gene sets, 864 were founders of hallmark signatures. We designated these vintage founder sets as ARCHIVED hidden collection and included in v5.2 MSigDB in order to preserve links to their pages from hallmark pages.</p>
<h2>Updates to C6 collection</h2>
<h2>Updates to C6 collection</h2>
Corrected typing errors in the names of two gene sets.
Corrected typing errors in the names of two gene sets.

Revision as of 21:29, 5 October 2016

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This page describes the changes made to the gene set collections for Release 5.2 of the Molecular Signatures Database (MSigDB).

Contents

Updates to C2:CGP - curated gene sets

We added 4 gene sets (submitted by Dr. Eppert, MgGill University) and redefined the gene set MCLACHLAN_DENTAL_CARIES_DN

Overhaul of C5 - gene ontology

Gene sets in this collection are derived from the controlled vocabulary of the Gene Ontology (GO) project: The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology (Nature Genet 2000). The gene sets are named by GO term and contain genes annotated by that term. We have deprecated the entire collection and define new gene sets using more recent GO term annotations.

This collection is divided into three subcollections:

  • CC: GO Cellular component (+584 gene sets). Gene sets derived from the Cellular Component Ontology.
  • MF: GO Molecular function (+929 gene sets). Gene sets derived from the Molecular Function Ontology.
  • BP: GO Biological process (+4653 gene sets). Gene sets derived from the Biological Process Ontology.

Among the deprecated C5 gene sets, 864 were founders of hallmark signatures. We designated these vintage founder sets as ARCHIVED hidden collection and included in v5.2 MSigDB in order to preserve links to their pages from hallmark pages.

Updates to C6 collection

Corrected typing errors in the names of two gene sets.

Updates to C7 collection

Corrected typing errors in the names of 332 gene sets and fixed other errors in gene set annotations.

For more information

For complete descriptions of all collections or to download the updated gene sets, go to the Browse Collections page. Detailed information about v5.1 MSigDB gene sets that have been renamed, deprecated or archived in the 5.2 release can be found here

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