Figure 2

A protein-protein interaction network of E. coli showing high-density complexes of size ≥ 3 detected by the proposed algorithm. Functions of the proteins of 10 largest complexes are as follows: complex 1, components of RNA polymerase (RpoA, RpoB, RpoC, Rsd, RpoZ RpoD, RpoN, FliA); complex 2, components of ATP synthetase (AtpA, AtpB, AtpE, AtpF, AtpG, AtpH, AtpL); complex 3, components of DNA polymerase (DnaX, HolA, HolB, HolD, and HolC); complex 4, proteins involved in cell division (FtsQ, FtsI, FtsW, FtsN, FtsK and FtsL); complex 5, components of ribonucleoside-diphosphate reductase (NrdA, NrdB, NrdE, NrdF); complex 6, chaperons (DnaK, GrpE, DnaI) and a heat-shock sigma factor (RpoH), complex 7, component of protein translocase (SecA, SecE, SecY, SecG); complex 8, DNA mismatch repair proteins (MutL, MutS, MutH, UvrD); complex 9, components of fumarate reductase (FrdA, FrdB, FrdC, FrdD); and complex 10, proteins associated with molybdopterin biosynthesis (MoeA, MoeB, MobB, Mog). 11 to 22 are 3-protein complexes, which mostly consist of similar function proteins.