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.

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:

1. Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC)
2. UniGene
3. 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
• v2.0 MSigDB (Jan 2007)

  The collection was replace with new set assignments after parsing annotations from

  • Oct 2006 release of HGNC
  • 27 Nov 2006 Homo sapiens Build #197 of UniGene
• v3.0 MSigDB (Sep 2010)

  sets with fewer than 10 genes were deprecated

• v3.1 MSigDB (Oct 2012)

  Set contents was updated after switching to human Entrez Gene IDs as the standard gene identifiers throughout the database. While total number of sets in C1 remained the same, this changed the contents of some individual sets.

C2: curated gene sets

Gene sets collected from various sources such as online pathway databases, scientific publications and personal contributions from domain experts. The gene set page for each gene set lists its source.

C3: motif gene sets

Gene sets group genes by cis-regulatory motifs. The motifs are catalogued in Xie et al. and represent known or putative conserved regulatory elements in promoters and 3’-UTR regions. These sets make it possible to link changes in a genomic experiment to a conserved, putative cis-regulatory elements.

C4: computational gene sets

Gene sets defined by mining large collections of cancer-oriented genes.

C5: GO gene sets

Gene sets are named by Gene Ontology (GO) terms and contain genes annotated by that term.

C6: oncogenetic signatures

Gene sets represent signatures of cellular pathways which are often dis-regulated in cancer. The majority of signatures were generated directly from microarray data from NCBI GEO or from in house unpublished expression profiling experiments which involved perturbation of known cancer genes. In addition, a small number of oncogenic signatures was curated from scientific publications.

C7: immunologic signatures

Gene sets that represent cell states and perturbations within the immune system. The signatures were generated by manual curation of published studies in human and mouse immunology. For each study, pairwise comparisons of relevant classes were made and genes ranked by mutual information. Gene sets correspond to top or bottom ranking genes (FDR < 0.25 or maximum of 200 genes) for each comparison. This resource is generated as part of the Human Immunology Project Consortium (HIPC).