This pipeline inspects significant overlapping pathway genesets for a given gene list using a hypergeometric test. For the gene set database, we uses GSEA MSigDB Class2: Canonical Pathways DB as a geneset data. Further details about the MsigDB genesets, please visit The Broad Institute GSEA MsigDB

For a given gene list, a hypergeometric test was tried to find significant overlapping canonical pathway gene sets. In terms of FDR adjusted p.values, top 5 significant overlapping gene sets are listed as below.

• KEGG_PATHWAYS_IN_CANCER, KEGG_PANCREATIC_CANCER, KEGG_PROSTATE_CANCER, KEGG_CHRONIC_MYELOID_LEUKEMIA, BIOCARTA_PPARA_PATHWAY

• Gene set database = c2.cp.v3.0-2.symbols.gmt

• Input gene list = sig_genes.txt

For a given gene list, it uses a hypergeometric test to get a significance of each overlapping pathway geneset. The hypergeometric p-value is obtained by R library function phyer() and is defined as a probability of randomly drawing x or more successes(gene matches) from the population consisting N genes in k(the input genes) total draws.

• a cumulative p.val with lower tail==T in phyer():

• ex). a probability to see at least 3 genes in the group is p(x>=3) = 1 - p(x<=2)= 1 - phyer(2, lower.tail=T) that is, f(x| N, m, k) = mCk * ((N-m) C (n-k)) / ((N) C (n))

• The hypergeometric test is identical to the corresponding one-tailed version of Fisher's exact test.

• ex). Fisher' exact test = matrix(c(n.Found, n.GS-n.Found, n.drawn-n.Found, n.NotGS- (n.drawn-n.Found)), nrow=2, dimnames = list(inputGenes = c("Found", "NotFound"),GeneUniverse = c("GS", "nonGS")) )

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

• Analysis Results (MD5 checksum)

• Auxiliary Data (MD5 checksum)

• MAGE-TAB File (MD5 checksum)