Difference between revisions of "MSigDB v5.1 Release Notes"
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| − | + | [http://www.broadinstitute.org/gsea/ GSEA Home] | | |
| + | [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | | ||
| + | [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | | ||
| + | [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] | | ||
| + | [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br> | ||
<br> | <br> | ||
<h2>Updates to C7: Immunologic Signatures</h2> | <h2>Updates to C7: Immunologic Signatures</h2> | ||
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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> | <p> | ||
| − | We first captured relevant microarray datasets published in the immunology literature that have raw data deposited to | + | We first captured relevant microarray datasets published in the immunology literature that have raw data deposited to [http://www.ncbi.nlm.nih.gov/geo 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.</p> |
<p>The C7 immunologic signatures collection (also called ImmuneSigDB) was generated as part of our collaboration with the | <p>The C7 immunologic signatures collection (also called ImmuneSigDB) was generated as part of our collaboration with the | ||
| − | + | [http://haining.dfci.harvard.edu Haining Lab] | |
at Dana-Farber Cancer Institute and the | at Dana-Farber Cancer Institute and the | ||
| − | + | [http://www.immuneprofiling.org Human Immunology Project Consortium (HIPC)].</p> | |
<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>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>Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. | ||
| − | <br>Immunity. 2016 Jan 19; 44(1): 194-206. | + | <br>Immunity. 2016 Jan 19; 44(1): 194-206. [http://www.ncbi.nlm.nih.gov/pubmed/26795250 PMID: 26795250]</p> |
<p> | <p> | ||
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<h2>Updates to C2 collection</h2> | <h2>Updates to C2 collection</h2> | ||
<h3>Updates to C2:CP collection</h3> | <h3>Updates to C2:CP collection</h3> | ||
| − | <p>Due to changes involving BioCarta, we have updated our external links for all gene sets from BioCarta. For more details, please refer to the | + | <p>Due to changes involving BioCarta, we have updated our external links for all gene sets from BioCarta. For more details, please refer to the [http://www.genecarta.com BioCarta announcement].</p> |
| + | |||
<h3>Updates to C2:CGP collection</h3> | <h3>Updates to C2:CGP collection</h3> | ||
| − | <p>Alerted by sharp-eyed users of MSigDB, we redefined 3 gene sets based on the publication in | + | <p>Alerted by sharp-eyed users of MSigDB, we redefined 3 gene sets based on the publication in [http://www.ncbi.nlm.nih.gov/pubmed/15897907 Oncogene 2005] by Farmer et al. In the process, we also brought back one gene set from this publication that has been deprecated since v3.1 MSigDB.</p> |
<h2>Updates to C4 collection</h2> | <h2>Updates to C4 collection</h2> | ||
<h3>Updates to C4:CM collection</h3> | <h3>Updates to C4:CM collection</h3> | ||
<p>We have enhanced brief descriptions of 150 cancer modules according to the information available in the original source of this sub-collection.</p> | <p>We have enhanced brief descriptions of 150 cancer modules according to the information available in the original source of this sub-collection.</p> | ||
Latest revision as of 07:41, 29 September 2016
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Contents
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 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.
The C7 immunologic signatures collection (also called ImmuneSigDB) was generated as part of our collaboration with the Haining Lab at Dana-Farber Cancer Institute and the Human Immunology Project Consortium (HIPC).
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. PMID: 26795250
Alerted by a very attentive user of our resource, we corrected errors in the annotations of a pair of gene sets.
Fixed errors in a number of other gene sets.
Updates to C2 collection
Updates to C2:CP collection
Due to changes involving BioCarta, we have updated our external links for all gene sets from BioCarta. For more details, please refer to the BioCarta announcement.
Updates to C2:CGP collection
Alerted by sharp-eyed users of MSigDB, we redefined 3 gene sets based on the publication in Oncogene 2005 by Farmer et al. In the process, we also brought back one gene set from this publication that has been deprecated since v3.1 MSigDB.
Updates to C4 collection
Updates to C4:CM collection
We have enhanced brief descriptions of 150 cancer modules according to the information available in the original source of this sub-collection.
