Difference between revisions of "MSigDB v5.1 Release Notes"
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<p>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>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> | ||
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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>. | ||
To cite your use of the collection, and for further information, please refer to <a href=http://www.cell.com/immunity/abstract/S1074-7613(15)00532-4> | To cite your use of the collection, and for further information, please refer to <a href=http://www.cell.com/immunity/abstract/S1074-7613(15)00532-4> | ||
this publication</a> | this publication</a> | ||
(Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte A, Mesirov JP, Haining WN, <i>Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammationi</i>, Immunity (2016): published online 12 Jan 2016.) | (Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte A, Mesirov JP, Haining WN, <i>Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammationi</i>, Immunity (2016): published online 12 Jan 2016.) | ||
Revision as of 18:47, 13 January 2016
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 <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 <a href=http://www.cell.com/immunity/abstract/S1074-7613(15)00532-4> this publication</a> (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 Inflammationi, Immunity (2016): published online 12 Jan 2016.)
