Algorithm 1

Greedy driver gene selection algorithm

Require: be the bipartite graph, where denotes the set of nodes corresponding to mutated genes, denotes the set of nodes corresponding to the patient-specific outlying expression events, and denotes the set of edges between and

1:

//the set of selected driver genes

2:

//the number of all the connected outlying expression events

3: z ← 0

//the number of covered outlying expression events so far

4: while z < Z do

5:

//pick mutated gene with the highest degree; in case of a tie, randomly pick one of the genes

6:

//update the number of covered outlying events

7:

//add g to the driver set

8:

9: for g' ∈ S do

10:

//remove the node g' and its connected edges from

11: end for

12: end while

13:

Bashashati et al. Genome Biology 2012 13:R124   doi:10.1186/gb-2012-13-12-r124