Difference between revisions of "MSigDB v5.1 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> | ||
| + | <br> | ||
<h2>Updates to C7: Immunologic Signatures</h2> | <h2>Updates to C7: Immunologic Signatures</h2> | ||
<p> | <p> | ||
We added to the C7 collection <strong>2,962 new gene sets </strong> derived directly from microarray data of immunological studies. 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> | We added to the C7 collection <strong>2,962 new gene sets </strong> derived directly from microarray data of immunological studies. 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>We first captured relevant microarray datasets published in the immunology literature that have raw data deposited to | + | <p>We first captured relevant microarray datasets published in the immunology literature that have raw data deposited to <a href="http://www.ncbi.nlm.nih.gov/geo">Gene Expression Omnibus (GEO)</a>. 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.</p> |
<p> | <p> | ||
| − | The C7 immunologic signatures collection (also called ImmuneSigDB) was generated as part of our collaboration with the <a href=http://haining.dfci.harvard.edu>Haining Lab</a> at Dana-Farber Cancer Institute and the <a href=http://www.immuneprofiling.org>Human Immunology Project Consortium (HIPC)</a>. | + | The C7 immunologic signatures collection (also called ImmuneSigDB) was generated as part of our collaboration with the <a href=http://haining.dfci.harvard.edu>Haining Lab</a> at Dana-Farber Cancer Institute and the <a href=http://www.immuneprofiling.org>Human Immunology Project Consortium (HIPC)</a>.</p> |
| − | To cite your use of the collection, and for further information, please refer to | + | <p> |
| − | + | To cite your use of the collection, and for further information, please refer to | |
| − | + | <br>Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte A, Mesirov JP, Haining WN. | |
| + | <br>Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. | ||
| + | <br>Immunity. 2016 Jan 19; 44(1): 194-206. <a href="http://www.ncbi.nlm.nih.gov/pubmed/26795250">PMID: 26795250</a></p> | ||
Revision as of 15:07, 1 February 2016
<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>
Updates to C7: Immunologic Signatures
We added to the C7 collection 2,962 new gene sets derived directly from microarray data of immunological studies. 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 <a href="http://www.ncbi.nlm.nih.gov/geo">Gene Expression Omnibus (GEO)</a>. 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.
The C7 immunologic signatures collection (also called ImmuneSigDB) was generated as part of our collaboration with the <a href=http://haining.dfci.harvard.edu>Haining Lab</a> at Dana-Farber Cancer Institute and the <a href=http://www.immuneprofiling.org>Human Immunology Project Consortium (HIPC)</a>.
To cite your use of the collection, and for further information, please refer to
Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte A, Mesirov JP, Haining WN.
Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.
Immunity. 2016 Jan 19; 44(1): 194-206. <a href="http://www.ncbi.nlm.nih.gov/pubmed/26795250">PMID: 26795250</a>
