Pathway-Driven Discovery of Rare Mutational Impact on Cancer

Algorithm 1

(1)   In the given pathway, define a “gene list”

(2)   gene list: gene names in the given pathway

(3)

(4)   for each gene in the “gene list” (𝑖 in 1 ~ size of gene list)

(5)   “candidate list” = “gene list” − gene[𝑖]

(6)     while (no more genes in the “candidate list” or

(7)     no more significant mutational event) {

(8)

(9)      update: gene(s) name(s) to be considered as mutational event

(11)      𝑥: a vector containing pathway statistics of patients with mutational event

(12)      𝑦: a vector containing pathway statistics of patients without mutational event

(13)

(14)      do t-test on 𝑥 and 𝑦

(15)      if  (𝑡-test 𝑞-value < threshold) {

(16)         add one more gene for mutational event

(17)      }

(18)      update the number of total iteration (this is used for 𝑞-value calculation)

(19)      remove the gene from the “candidate list”

(20)    }

(21)   }