BioMed Research International / 2012 / Article / Alg 1

Research Article

MOfinder: A Novel Algorithm for Detecting Overlapping Modules from Protein-Protein Interaction Network

Algorithm 1

Input: The PPI network 𝐺 = ( 𝑉 , 𝐸 ) ;
   Cluster coefficient threshold CC;
   Sliding window 𝑠 .
   Output: modules.
   (1) 𝑀 = zeros ( 𝑉 , 𝑉 ) ; // initialization of network matrix
   (2) for each 𝑒 ∈ 𝐸   do
   (3)     𝑀 ( 𝑒 1 , 𝑒 2 ) = 1 ; // build sparse matrix, 𝑒 1 ∈ 𝑉 , 𝑒 2 ∈ 𝑉
   (4) end for
   (5) Mg = global AMD( 𝑀 );
   (6) While π‘Ž + 𝑠 β©½ 𝑉   do // π‘Ž = 1 , as start
   (7)    mg = Mg ( π‘Ž ∢ π‘Ž + 𝑠 , π‘Ž ∢ π‘Ž + 𝑠 ) ;
   (8)    ml = local AMD(mg);
   (9)    if cc (ml) β©Ύ CC do
(10)       insert ml to modules;
(11)    end if
(12)     π‘Ž = π‘Ž + 1 ;
(13) end while
(14) for each module 𝐴 in modules do
(15)    if module 𝐴 ∈ module 𝐡 do // module 𝐡 in modules and module 𝐴 β‰  module 𝐡
(16)       discard module 𝐴 from modules; // delete redundancy
(17)    end if
(18) end for

Article of the Year Award: Outstanding research contributions of 2020, as selected by our Chief Editors. Read the winning articles.