Gene Set Analysis

      Software and resources
         for inference on gene sets in microarray studies



Main references

The Gene Set Enrichment paper:

  • Subramanian, A. and Tamayo, P. Mootha, V. K. and Mukherjee, S. and Ebert, B. L. and Gillette, M. A. and Paulovich, A. and Pomeroy, S. L. and Golub, T. R. and Lander, E. S. and Mesirov, J. P. (2005). A knowledge-based approach for interpreting genome-wide expression profiles. PNAS. 102, pg 15545-15550.

    Our followup paper:

  • Bradley Efron and Rob Tibshirani. Tech report. August 2006
    On testing the significance of sets of genes (ps file)
    (pdf file)

    How does Gene set analysis differ from Gene set enrichment analysis?



    Software:

  • R software package GSA: Linux version
    Windows version

  • Excel Add-in in SAM version 3.0- to come

    Available gene set collections:

    These are .gmt files- tab-delimited text. Stanford collection prepared by Kang Liu.

  • MSigDb collection from the Broad institute; You must register on their site before downloading the geneset (.gmt) files

  • Tissues gene sets from Stanford Microarray Database; A description is available at Synthetic genes page on SMD

  • Cellular processes gene sets from Stanford Microarray Database; A description is available at Synthetic genes page on SMD

  • Cytobands from Stanford Microarray Database; A description is available at Synthetic genes page on SMD

  • Chromosome Arms from Stanford Microarray Database; A description is available at Synthetic genes page on SMD

  • 5MbChromosomalTiles from Stanford Microarray Database; A description is available at Synthetic genes page on SMD

  • Cancer module gene sets from Eran Segal's lab; A description is available at Eran Segal's cancer modules site