Algorithm 1: Algorithm for module extraction from gene gene network

Input: A = {V, E} (Gene gene network); CCT (Clustering coefficient threshold); SST (Semantic similarity threshold); NSS (Semantic similarity score matrix)

Output: Modules = {C 1, C 2, …, C N}, (a set of N modules)

1 Initialize clusterExpNode = V, Modules = NULL;

2      while |clusterExpNode| > 4 do

3          choose $v_m\in clusterExpNode$ such that $\forall v_n\in clusterExpNode$, CC(v m) ≥ CC(v n) and CC(v m) ≥ CCT; $partialCluster=partialCluster\cup v_m$;

4          while v m exists do

5                   choose another v i from $N_{s(v_m)}$ if and only if $\exists v_x\in partialCluster$ such that NSS(v i, v x) ≥ SST

6                   $partialCluster=partialCluster\cup v_i$;

7                   clusterExpNode = clusterExpNode − v i;

8                   $N_{s(v_m)}=\left(N_{s(v_m)}\cup N_{s(v_i)}\right)$ choose next v i;

9          end

10          Mark partialCluster as C count only when |partialCluster| ≥ 3;

11          $Modules=Modules\cup C_{count}$;

12          count + +;

13      end

14 Return Modules;