Advertisement

A Description of the Molecular Signatures Database (MSigDB) Web Site

  • Arthur LiberzonEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1150)

Abstract

Annotated lists of genes help researchers to prioritize their own lists of candidate genes and to plan follow-up studies. The Molecular Signatures Database (MSigDB) is one of the most widely used knowledge base repositories of annotated sets of genes involved in biochemical pathways, signaling cascades, expression profiles from research publications, and other biological concepts. Here we provide an overview of MSigDB and its online analytical tools.

Key words

Bioinformatics Database Genomics Molecular sequence annotation Gene expression profiling 

References

  1. 1.
    Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102(43):15545–15550PubMedCentralPubMedCrossRefGoogle Scholar
  2. 2.
    Liberzon A, Subramanian A, Pinchback R, Thorvaldsdóttir H, Tamayo P, Mesirov JP (2011) Molecular signatures database (MSigDB) 3.0. Bioinformatics 27(12):1739–1740PubMedCentralPubMedCrossRefGoogle Scholar
  3. 3.
    Rivals I, Personnaz L, Taing L, Potier MC (2007) Enrichment or depletion of a GO category within a class of genes: which test? Bioinformatics 23(4):401–417PubMedCrossRefGoogle Scholar
  4. 4.
    Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol 57(1):289–300Google Scholar
  5. 5.
    Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101(16):6062–6067PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov JP, Poggio T, Gerald W, Loda M, Lander ES, Golub TR (2001) Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci USA 98(26):15149–15154PubMedCentralPubMedCrossRefGoogle Scholar
  7. 7.
    Shankavaram UT, Reinhold WC, Nishizuka S, Major S, Morita D, Chary KK, Reimers MA, Scherf U, Kahn A, Dolginow D, Cossman J, Kaldjian EP, Scudiero DA, Petricoin E, Liotta L, Lee JK, Weinstein JN (2007) Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study. Mol Cancer Ther 6(3):820–832PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Broad Institute of MIT and Harvard301 Binney StreetCambridgeUSA

Personalised recommendations