Difference between revisions of "MSigDB Acknowledgements"

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<p>The Molecular Signature Database (MSigDB) is a collection of gene sets maintained by the GSEA team. The team welcomes and appreciates contributions to this shared resource and encourages users to submit their gene sets to mailto:gsea@broad.mit.edu. The MSigDB contains four categories of genes sets. Our thanks to the contributors.</p>
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[http://www.broadinstitute.org/gsea/ GSEA Home] |
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[http://www.broadinstitute.org/gsea/downloads.jsp Downloads] |
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[http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] |
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[http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |
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[http://www.broadinstitute.org/gsea/contact.jsp Contact]
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See the page [http://software.broadinstitute.org/gsea/msigdb/collection_details.jsp MSigDB Collections: Details and Acknowledgments] on the main website.
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o:href="http://www.broad.mit.edu/gsea/images/bullet.gif" />
 
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</v:shape><![endif]--><!--[if !vml]--><img width="16" height="6" border="0" alt="" src="file:///C:%5CDOCUME~1%5Chkuehn%5CLOCALS~1%5CTemp%5Cmsohtml1%5C01%5Cclip_image001.gif" v:shapes="_x0000_i1025" /><!--[endif]-->&nbsp;&nbsp; <strong>Category C1, Positional (chromosomal location):</strong> Contains 24 gene sets corresponding to the genes on each of the 24 human chromosomes, as well as 301 sets corresponding to cytogenetic bands. These gene sets can be helpful in identifying effects related to epigenetic silencing, dosage compensation, copy number polymorphisms, and aneuploidy or other chromosomal deletions/amplifications. </p>
 
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</v:shape><![endif]--><!--[if !vml]--><img width="16" height="6" border="0" alt="" src="file:///C:%5CDOCUME~1%5Chkuehn%5CLOCALS~1%5CTemp%5Cmsohtml1%5C01%5Cclip_image001.gif" v:shapes="_x0000_i1026" /><!--[endif]-->&nbsp;&nbsp; <strong>Category C2, Curated (functional):</strong> Contains gene sets of metabolic and signaling pathways gleaned from the following publicly available manually curated databases:</p>
 
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    <li class="MsoNormal" style=""><span lang="FR" style="">BioCarta: http://www.biocarta.com/<o:p></o:p></span></li>
 
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    <li class="MsoNormal" style="">Signaling pathway database:      http://www.grt.kyushu-u.ac.jp/spad/menu.html</li>
 
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    <li class="MsoNormal" style="">Signaling gateway:      http://www.signaling-gateway.org/</li>
 
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    <li class="MsoNormal" style="">Signal transduction knowledge      environment: http://stke.sciencemag.org/</li>
 
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    <li class="MsoNormal" style="">Human protein reference      database: http://www.hprd.org/</li>
 
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    <li class="MsoNormal" style="">GenMAPP:      http://www.genmapp.org/</li>
 
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    <li class="MsoNormal" style="">Gene ontology:      http://www.geneontology.org/</li>
 
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    <li class="MsoNormal" style="">Sigmal Aldrich pathways:      http://www.sigmaaldrich.com/Area_of_Interest/Biochemicals/Enzyme_Explorer/Key_Resources.html</li>
 
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    <li class="MsoNormal" style="">Gene arrays, BioScience      corporation: http://www.superarray.com/</li>
 
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    <li class="MsoNormal" style="">Human cancer genome anatomy      consortium: http://cgap.nci.nih.gov/</li>
 
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    <li class="MsoNormal" style="">L2L, John Newman and Alan      Weiner, Department of Biochemistry, <st1:place w:st="on"><st1:placetype w:st="on">University</st1:placetype> of <st1:placename w:st="on">Washington</st1:placename></st1:place>. http://depts.washington.edu/l2l/</li>
 
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<p>In addition, contains gene sets representing gene expression signatures of genetic and chemical perturbations that have been culled from experimental results in the literature. </p>
 
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</v:shape><![endif]--><!--[if !vml]--><img width="16" height="6" border="0" alt="" src="file:///C:%5CDOCUME~1%5Chkuehn%5CLOCALS~1%5CTemp%5Cmsohtml1%5C01%5Cclip_image001.gif" v:shapes="_x0000_i1027" /><!--[endif]-->&nbsp;&nbsp; <strong>Database C3, Motif (motif-based):</strong> Each gene set in this category contains genes that lie downstream of a motif that is conserved across the human, mouse, rat, and dog genomes. The motifs are catalogued in [http://wwwdev.broad.mit.edu/gsea/doc/xie05_motif_paper.pdf Xie, et al, 2005] and [http://wwwdev.broad.mit.edu/gsea/doc/xie05_motif_paper_supp_info.pdf Supplemental Information] and represent known or likely regulatory elements in promoters and 3'-untranslated regions. </p>
 
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</v:shape><![endif]--><!--[if !vml]--><img width="16" height="6" v:shapes="_x0000_i1025" src="file:///C:%5CDOCUME~1%5Chkuehn%5CLOCALS~1%5CTemp%5Cmsohtml1%5C01%5Cclip_image001.gif" alt="" /><!--[endif]-->&nbsp;&nbsp; <strong>Database C4, Computed (correlational): </strong>Correlation gene sets are groups of genes defined by computationally mining large-scale experimental datasets for co-expressed genes.</span>
 

Latest revision as of 20:04, 5 April 2017

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See the page MSigDB Collections: Details and Acknowledgments on the main website.

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