An Algorithm for Finding Functional Modules and Protein Complexes in Protein-Protein Interaction Networks

Algorithm 1

AssignNearCliqueIdx.

(1) for all node 𝑁∈𝐺 do

(2)  𝑁.𝑐𝑙𝑑𝑥=0                         {initialize cIdx of all nodes to 0}

(3) end for

(4) 𝑐𝑢𝑟𝐶𝐼𝑑𝑥=1                        {set the current clique index to 1}

(5) for all node 𝑁∈𝐺 do

(6)  if (isClique(𝑁)) then {if the node 𝑁 belongs to a clique}

(7)   for all edge 𝐸∈𝑁 do

(8)    if (𝐸.target.𝑐𝐼𝑑𝑥>0) then {if the 𝑐𝐼𝑑𝑥 of the node connected to 𝑁 is positive}

(9)     for all 𝑡𝑚𝑝𝑁∈𝐺 do {for all nodes in 𝐺 }

(10)      if (𝑡𝑚𝑝𝑁.𝑐𝐼𝑑𝑥=𝐸.target.𝑐𝐼𝑑𝑥) then

(11)      𝑡𝑚𝑝𝑁.𝑐𝐼𝑑𝑥=𝑐𝑢𝑟𝐶𝐼𝑑𝑥     {assign 𝑐𝑢𝑟𝐶𝐼𝑑𝑥 to 𝑡𝑚𝑝𝑁 as its cIdx}

(12)      end if

(13)     end for

(14)    else

(15)     𝐸.target.𝑐𝐼𝑑𝑥=𝑐𝑢𝑟𝐶𝐼𝑑𝑥

(16)    end if

(17)   end for

(18)    𝑁.𝑐𝐼𝑑𝑥=𝑐𝑢𝑟𝐶𝐼𝑑𝑥                 {set 𝑐𝐼𝑑𝑥 of 𝑁 to 𝑐𝑢𝑟𝐶𝐼𝑑𝑥 }

(19)   𝑐𝑢𝑟𝐶𝐼𝑑𝑥++                     {increase 𝑐𝑢𝑟𝐶𝐼𝑑𝑥 by one}

(20)  end if

(21) end for