Sub-GSE: Testing Gene Set Enrichment for Subset of Genes

Program:

Our program have been implemented in a program by C++, here are the pre-complied executable files:

  • The executable file for Windows OS (Windows 95/98/2000/NT/XP,32-bit, 64-bit)
  • The executable file for Linux OS (32-bit, 64-bit)

 

After downloading the file, please unzip it. A brief Help File (PDF format) for how to use this program can also be downloaded.

 

Attention: This program is free for academic use. The commercial users should contact Dr. Sun before using this program. The source code of the program has not been provided and may be available upon request.

Sample Data Sets:

Male vs. Female Data Set

Sample input file: gender.zip which contains the following files.

  • Gender_SubGSE.txt - contains the Male vs Female Lymphoblastoid cells data of 15056 genes across 32 individuals.
  • Gender.cls - contains the phenotypic data indicating the gender of the 32 individuals.
  • C1.gmt - contains gene sets C1 from MSigDB.
  • C2.gmt - contains gene sets C2 from MSigDB.

Sample output files:

  • Gender_C1.txt - contains the p-values of all C1 gene sets by SubGSE.
  • Gender_C2.txt - contains the p-values of all C2 gene sets by SubGSE.

 

The q-values in the paper were calculated by applying the QVALUE R package to the p-values in Gender_C1.txt and Gender_C2.txt.

 

Attention: Please convert format of your data file

P53 Mutational Status Data Set

Sample input file: p53_data.zip which contains the following files

  • p53_SubGSE.txt - contains the gene expression levels of 10100 genes in 50 cancer cell lines.
  • P53.cls - contains the phenotypic data describing the mutational status of p53 (carrying any p53 mutation or not) for the 50 cell lines.
  • C2.gmt - contains gene sets C2 from MSigDB.

Sample output files:

  • p53_C2.txt – contains the p-values of all C2 gene sets by SubGSE.

 

The q-values in the paper were calculated by applying the QVALUE R package to the p-values in Gender_C1.txt and Gender_C2.txt.

 

Please contact us if there are any bugs within our program. 
Copyright © 2005 The University of Southern California. All RIGHTS RESERVED.

Created Date: April 2008
Last Updated Date: April 1, 2008
Contact

 Fengzhu Sun, Ph.D.
 Molecular and Computational Biology Program
 Department of Biological Sciences
 University of Southern California
 Los Angeles, CA, 90089
 (213) 740-2413 (phone)
 (213) 740-2424 (fax)
 Email: fsun AT usc DOT edu