MSigDB collections
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This page provides detailed descriptions of all collections of gene sets in MSigDB.
To learn about changes and other information specific for a particular release of MSigDB, please refer to the corresponding Release_Notes.
Contents
H: Hallmarks
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C1: positional gene sets
Genes from the same genomic location (chromosome or cytogenetic band) are grouped in a gene set. Cytogenetic annotations are from three sources:
- Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC)
- UniGene
- Affymetrix microarray annotations
We merged the relevant annotations from these resources and derived a single cytogenetic band location for every gene symbol. These were then grouped into sets. Decimals in cytogenetic bands were ignored. For example, 5q31.1 was considered 5q31. Therefore, genes annotated as 5q31.2 and those annotated as 5q31.3 were both placed in the same set, 5q31.
When there were conflicts, the UniGene entry was used.
These sets are helpful in identifying effects related to chromosomal deletions or amplifications, dosage compensation, epigenetic silencing, and other regional effects.
Revision history
- v1.0 MSigDB (Mar 2005) first appearance of C1 collection. It contained 24 sets, one for each of the 24 human chromosomes, and 295 sets corresponding to cytogenetic bands.
- v1.1 MSigDB (Nov 2005) the collection was replaced with new set assignments after parsing annotations from
- Oct 2005 release of HGNC
- 20 Jan 2005 Homo sapiens Build #180 of UniGene
- 19 Sep 2005 release of Affymetrix annotations for human chips
C2: curated gene sets
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C3: motif gene sets
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C4:computational gene sets
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C5: GO gene sets
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C6: oncogenetic signatures
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C7: immunologic signatures
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