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The MSigDB Cancer Neighborhood

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1 ontology contains gene sets from mining large collections of cancer-oriented microarray data. Each gene set is defined by correlated expression with one of 380 cancer-associated genes2 .


The human hg19 ontology contains 427 gene sets, 4,351 genes, and 38,586 total term <--> gene associations.

The human hg18 ontology contains 427 gene sets, 4,363 genes, and 38,679 total term <--> gene associations.


All data for this ontology was downloaded on September 30, 2010 (MSigDB version 3.0).

GREAT v1.2

GREAT v1.2 MSigDB Cancer Neighborhood statistics are available here.


Ref Notes
1 Subramanian, A., et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc Natl Acad Sci U S A. 2005 Oct 25; 102(43):15545-50.
2 Brentani, H., et al. The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags, Proc Natl Acad Sci U S A. 2003 Nov 11; 100(23):13418-23.
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