Difference between revisions of "MSigDB v5.0 Release Notes"
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<h3>Updates to C2:CGP collection</h3> | <h3>Updates to C2:CGP collection</h3> | ||
<p>In response to requests from multiple users of our resource, we removed all 7 gene sets based on the publication in [http://www.ncbi.nlm.nih.gov/pubmed/17057710 Nat Med 2006] by Patti et. al, which has been retracted.</p> | <p>In response to requests from multiple users of our resource, we removed all 7 gene sets based on the publication in [http://www.ncbi.nlm.nih.gov/pubmed/17057710 Nat Med 2006] by Patti et. al, which has been retracted.</p> | ||
| − | <p>Alerted by sharp-eyed users of MSigDB, we redefined four gene sets based on the publication in [http://www.ncbi.nlm.nih.gov/pubmed/20129251 Cancer Cell 2010] by Verhaak et al. | + | <p>Alerted by sharp-eyed users of MSigDB, we redefined four gene sets based on the publication in [http://www.ncbi.nlm.nih.gov/pubmed/20129251 Cancer Cell 2010] by Verhaak et al.</p> |
| + | <p>At request of Dr. Durand, with have updated records of two gene sets he contributed earlier.</p> | ||
| + | <p>Fixed errors in a number of other gene sets.</p> | ||
| + | <p>All these changes are documented here.</p> | ||
<h2>Changes in the XML file format</h2> | <h2>Changes in the XML file format</h2> | ||
Revision as of 20:35, 16 March 2015
<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>
Contents
New collection H: Hallmark signatures
H: Hallmarks is a new collection of 50 sets. These gene sets represent specific well defined biological states or processes and display coherent expression. The hallmark gene sets were generated by a computational methodology based on identifying gene set overlaps and extracting coherent representatives of them. Details of the procedure will become available after the manuscript describing it is accepted for publication. The hallmark gene sets reduce noise and redundancy and provide a better biological space for GSEA and other gene set-based analyses of genomic data.
We envision this collection as the starting point for exploring MSigDB resource and GSEA. This collection is an initial release of 50 hallmarks which condense information from over 4,000 original overlapping gene sets from v4.0 MSigDB collections C1 through C6. We refer to the original gene sets as “founder” sets.
Hallmark gene set pages provide links to the corresponding founder sets for more in-depth exploration. In addition, hallmark gene set pages include links to microarray data that served for refining and validation of the hallmark signatures.
Updates to C2 collection
C2:CP Matrisome gene sets
Updates to C2:CGP collection
In response to requests from multiple users of our resource, we removed all 7 gene sets based on the publication in Nat Med 2006 by Patti et. al, which has been retracted.
Alerted by sharp-eyed users of MSigDB, we redefined four gene sets based on the publication in Cancer Cell 2010 by Verhaak et al.
At request of Dr. Durand, with have updated records of two gene sets he contributed earlier.
Fixed errors in a number of other gene sets.
All these changes are documented here.
Changes in the XML file format
Viewing previous versions of MSigDB
Files from previous versions of MSigDB (v4.0, v3.1, v3.0, v2.5, v2.1 and v1.0) are archived and available at Downloads page. You can view them through the MSigDB Browser tool in the GSEA desktop application.
