Differential gene set enrichment analysis in genome-wide mutational data

A computer program product for analyzing genomic data, the computer program product comprising:

• a computer readable storage medium readable by a processing circuit and storing program instructions for execution by the processing circuit for performing a method comprising:
• receiving genomic data for an organism and sample phenotypes R and R′;
• receiving a plurality of gene sets, wherein each of the gene sets includes genes associated with an attribute;
• for each of the plurality of gene sets:
• determining a set of genes G corresponding to genes in the gene set and a set of genes G′ corresponding to genes outside the gene set for the phenotypes R and R′;
• determining a set of mutated genes M and a set of non-mutated genes M′ for the phenotypes R and R′ and a mutation enrichment score;
• determining a set of differentiated genes D a set of non-differentiated genes D′ for the phenotypes R and R′;
• and
• identifying an enriched gene set GE based at least in part upon the mutation enrichment score and the differentiation enrichment score, wherein the GE corresponds to the set of genes G that is statistically enriched for D and M in the phenotype R.

A processing system for analyzing genomic data, comprising:

• a processor in communication with one or more types of memory, the processor configured to perform a method comprising:
• receiving genomic data for an organism and sample phenotypes R and R′;
• receiving a plurality of gene sets, wherein each of the gene sets includes genes associated with an attribute;
• for each of the plurality of gene sets:
• determining a set of genes G corresponding to genes in the gene set and a set of genes G′ corresponding to genes outside the gene set for the phenotypes R and R′;
• determining a set of mutated genes M and a set of non-mutated genes M′ for the phenotypes R and R′ and a mutation enrichment score;
• determining a set of differentiated genes D a set of non-differentiated genes D′ for the phenotypes R and R′;
• and
• identifying an enriched gene set GE based at least in part upon the mutation enrichment score and the differentiation enrichment score, wherein the GE corresponds to the set of genes G that is statistically enriched for D and M in the phenotype R.