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| − | <p class="MsoNormal">This page describes the changes made to the gene set collections for Release 2.1 of the Molecular Signatures Database (MSigDB).</p> | + | < a href=" http:// www. broad. mit. edu/ gsea/"> GSEA Home</ a> | <a href="http://www. broad. mit. edu/ gsea/ downloads. jsp"> Downloads</ a> | < a href=" http:// www. broad. mit. edu/ gsea/ msigdb/"> Molecular Signatures Database</a> | Documentation | <a href="http://www. broad. mit. edu/ gsea/ contact. jsp"> Contact</ a> < br /> |
| − | <p class="MsoNormal"><o:p> </o:p></p>
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| − | <h3>C1: Positional gene sets</h3>
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| − | <p class="MsoNormal">No changes were made.</p>
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| − | <h3>C2: Curated gene sets (+205)</h3>
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| − | <p class="MsoNormal">Gene sets from two sources were added to the C2 collection:</p>
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| − | <p class="MsoListBullet"><!--[if !supportLists]--><span style="font-size: 8pt;"><span style="">■<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span></span><!--[endif]-->CPG: chemical and genetic perturbations (+5 gene sets). Gene sets by Bild et al. (<em>Nature</em> <strong>439</strong>, 353 – 357, 2006) based on microarray analysis of expression profiles of key oncogenes in a model system where expression of these oncogenes transformed otherwise quiescent cells.</p>
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| − | <p class="MsoListBullet"> <!--[if !supportLists]--><span style="font-size: 8pt;"><span style="">■<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </ span></span></span><!--[endif]--> CP: canonical pathways (+200 gene sets). Gene sets from the KEGG PATHWAY (<a href="http://www. genome.jp/kegg/">http://www.genome.jp/kegg/</a>) database of molecular interaction and reaction networks for metabolism, various cellular processes, and human diseases.</p> | |
| − | <p class="MsoNormal">In addition, links to GenMAPP have been corrected. Specifically, on gene set cards for gene sets from GenMAPP, in the <em style="">External links</em> section, links broken due to GenMAPP updates have been corrected.</p>
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| − | <h3>C3: Motif gene sets</h3>
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| − | <p class="MsoNormal">No changes were made.</p>
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| − | <h3>C4: Computational gene sets (+456)</h3>
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| − | <p class="MsoNormal">C4 now contains two subcollections:</p>
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| − | <p class="MsoListBullet"><!--[if !supportLists]--><span style="font-size: 8pt;"><span style="">■<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span></span><!--[endif]-->CGN: cancer gene neighborhoods (+0 gene sets). Gene sets defined by expression neighborhoods centered on 380 cancer-associated genes (Brentani, Caballero et al. 2003). This is the C4 collection from the previous MSigDB release.</p> | |
| − | <p class="MsoListBullet"><!--[if !supportLists]--><span style="font-size: 8pt;"><span style="">■<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span></span><!--[endif]-->CM: cancer modules (+456 gene sets). <span class="blacksml">Gene sets defined by </span>Segal et al. (<span class="blacksml"><em>Nature Genetics</em> <strong>36</strong>, 1090 – 1098, 2004). Briefly, the authors compiled gene sets (‘modules’) from a variety of resources such as KEGG, GO, and others. By mining a large compendium of cancer-related microarray data, they identified 456 such modules as </span>significantly changed in a variety of cancer conditions.</p>
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| − | <h3>C5: GO gene sets (+1454)</h3>
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| − | <p class="MsoNormal">Gene sets in this new collection are derived from the controlled vocabulary of the Gene Ontology (GO) project: <span class="author"><em>The Gene Ontology Consortium.</em></span><cite> </cite><span class="title"><em>Gene Ontology: tool for the unification of biology.</em></span><cite> </cite><span class="journal"><em>Nature Genet.</em></span><cite> (2000) </cite><span class="volume"><em>25:</em></span><cite> 25-29</cite><cite><span style="font-style: normal;"> (</span></cite><a href="http://www. geneontology.org/">http://www. geneontology. org/ </ a>). The gene sets are named by GO term and contain genes annotated by that term.</p> | |
| − | <p class="MsoNormal"><strong style=""><o:p> </o:p></strong></p>
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| − | <p class="MsoNormal">This collection is divided into three subcollections:</p>
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| − | <p class="MsoListBullet"><!--[if !supportLists]--><span style="font-size: 8pt;"><span style="">■<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span></span><!--[endif]-->CC: GO Cellular component (+233 gene sets). Gene sets derived from the Cellular Component Ontology.</p>
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| − | <p class="MsoListBullet"><!--[if !supportLists]--><span style="font-size: 8pt;"><span style="">■<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span></span><!--[endif]-->MF: GO Molecular function (+396 gene sets). Gene sets derived from the Molecular Function Ontology.</p>
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| − | <p class="MsoListBullet"><!--[if !supportLists]--><span style="font-size: 8pt;"><span style="">■<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span></span><!--[endif]-->BP: GO Biological process (+825 gene sets). Gene sets derived from the Biological Process Ontology.</p>
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| − | <p class="MsoNormal"><strong style="">GSEA users</strong>: Gene set enrichment analysis identifies gene sets consisting of <em style="">co-regulated</em> genes; GO gene sets are based on ontologies and do <em style="">not</em> generally consist of co-regulated genes.</p>
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| − | <h3>For more information</h3>
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| − | <p class="MsoNormal">For complete descriptions of all collections, see the Molecular Signatures Database page.</p>
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| − | <p class="MsoNormal">To download the updated gene sets, go to the Browse Collections page.</p>
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