Identifying Dynamic Protein Complexes Based on Gene Expression Profiles and PPI Networks

Algorithm 2

The description of algorithm DPC.

Algorithm DPC

Input: 𝐺(𝑉,𝐸): a PPI network; Ge: gene expression data;

𝑇_𝑔: the threshold of gene expression; 𝑇_𝑑: the threshold of density.

Output: PC: protein complexes

(1) Call DetectingPPC;

(2) 𝑃_𝑅=𝑉−𝑃_𝐴;

(3) For each node 𝑣_𝑖∈𝑃_𝑅  do

      For all 𝐶_𝑗∈PPC do

       Compute CL(𝑣_𝑖,𝐶_𝑗)=∑_{𝑢∈𝐶𝑗}ECC(𝑢,𝑣);

       if CC(𝑣_𝑖,𝐶_𝑗)>0 then

      𝐼(𝑣_𝑖)=𝑗∣max CL(𝑣_𝑖,𝐶_𝑗);

(4) For each time course 𝑡  do

      For each node 𝑢∈𝑃_𝑅  do

       if Ge(𝑢,𝑡)≥𝑇_𝑔

        𝑗=𝐼(𝑢);

        𝐴_𝑇(𝑗,𝑡)=𝐴_𝑇(𝑗,𝑡)∪{𝑢};

      For each core 𝐶_𝑗∈PPC  do

       PC = PC ∪ 𝐶_𝑗∪𝐴_𝑇𝑗,𝑡;

(5) Filtering PC

(6) Output PC