Gene Set Pages

Each gene set in the MSigDB (Molecular Signature Database) is fully described by a gene set card. To review the gene set cards, click here. Or, from within the GSEA application, use the Browse MSigDB page (msigdb_browser) to browse the gene sets and to display their gene set cards.

Each gene set card contains the following information:

Standard name: Gene set name.

Systematic name: Internal identifier for the gene set, which consists of three parts:

▪         Category: Positional (C1), Curated (C2), Motif (C3), or Computed (C4).

▪         Subcategory: for C1, always Cytogenic; for C2, Animal Model, Clinical, Experimental pertuberation, Expert curation, Misc, Ontology, Pathway database, or Review paper; for C3, Representative motifs or Transfac; and for C4, always Neighborhood.

▪         Number: a unique number with the category:subcategory classification.

Brief description: A brief description of the gene. This is the description that appears on the Browse MSigDB page of the GSEA application.

Category: The category of the gene set, as defined above.

Sub-category: The subcategory of the gene set, as defined above.

Full description or Abstract: A more complete description of the gene set. For example, for gene sets linked to a PubMed entry, this field shows the abstract of that entry.

Publication URL: When available, a link to the source publication. For example, for gene sets linked to a PubMed entry, this is a link to the Entrez record of the source publication.

External links: When available, links to external websites that contain more information about the gene set.

Keywords & MeSH headings: Keywords derived from MeSH National Library of Medicine and/or manually entered.

Organism: The organism that the experiment was conducted in (generic for canonical pathways and ontologies).

Contributed by: Name of the person (or external database; for example, KEGG) who collected the gene set.

Source platform: Microarray platform that was used for expression profiling (for example, Affymetrix HU6800). Gene_Symbol is used if the gene set was not tied to a specific experiment (for example, for ontologies or a gene set from a review article).

Download: Links to download the gene set in different formats:

▪         grp: lists the genes in the gene set in plain text format

▪         xml: gene set definition formatted with structure annotation

▪         map: lists the genes in the gene set with details of the mapping between the originally reported accessions and their HUGO gene symbols

Genes: Displays the number of genes (HUGO gene symbols) and accessions (native accessions) in this gene set; if each native accession mapped to a unique HUGO gene symbol, these values are identical. Click the Toggle View link to show/hide the genes in the gene set along with their descriptions and links to external websites for gene-centric information.