Archived: SCSig collection: Signatures of Single Cell Identities

This page is preserved for historical purposes. An updated version of this collection was included in the MSigDB 7.2 Release as Collection 8. Please see the MSigDB 7.2 Release Notes for a description of the changes.

MSigDB has developed a preliminary collection of gene sets of cell identity markers for cell types from primarily normal human tissues. The gene sets were derived by curation of cluster markers from single-cell RNA experiments. These gene sets are intended to facilitate the assignment of primary cell types in datasets such as those from experiments developing organoids.

This initial release contains 256 signatures representing a preliminary collection of cell types from GI Tract, Pancreas, Kidney, Liver, Immune system, Retina and Brain.

MSigDB uses Ensembl as the platform annotation authority. Identifiers for genes are mapped to their HGNC approved Gene Symbol and NCBI Gene ID through annotations extracted from Ensembl's BioMart data service, as described in the MSigDB 7.0 Release Notes. To use these gene sets with GSEA, download a GMT (symbols is recommended) and use the GSEA Load Data screen to access.

For further information please refer to the gene sets respective publications (see metadata). To cite your use of the collection, please reference the GSEA-MSigDB website and the respective publication.

Funding for development of these gene sets was provided by the Collaborative Computational Tools for the Human Cell Atlas program sponsored by the Chan Zuckerberg Initiative.

SCSig v1.0.1:
mapped with Ensembl 99
(metadata unchanged from v1.0)
SCSig gene sets, gene symbols scsig.all.v1.0.1.symbols.gmt
SCSig gene sets, NCBI (Entrez) IDs scsig.all.v1.0.1.entrez.gmt
SCSig v1.0:
mapped with Ensembl 97
SCSig gene sets, gene symbols scsig.all.v1.0.symbols.gmt
SCSig gene sets, NCBI (Entrez) IDs scsig.all.v1.0.entrez.gmt
SCSig gene sets metadata, tabular Excel format scsig.v1.0.metadata.xls
SCSig gene sets metadata, text file format scsig.v1.0.metadata.txt