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, no significant overlapping gene sets are found.

Gene set database = c2.cp.v3.02.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 pvalue 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 * ((Nm) C (nk)) / ((N) C (n))

The hypergeometric test is identical to the corresponding onetailed version of Fisher's exact test.

ex). Fisher' exact test = matrix(c(n.Found, n.GSn.Found, n.drawnn.Found, n.NotGS (n.drawnn.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.