Figure 7
An overlap between a network cluster obtained by Potts algorithm [31] and the best matching GO groups from the biological function GOA combined from MedScan annotation and public annotation. The cluster contains nine proteins involved in DNA repair and telomere capping: ATM – ataxia telangiectasia mutated homolog (human) (mapped); PRKDC – catalytic polypeptide of DNA activated protein kinase; NBS1 – nibrin; CHEK2 – protein kinase Chk2; XRCC5 – X-ray repair complementing defective repair in Chinese hamster cells 5; H2AFX – dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase); G22P1 – thyroid autoantigen; NFBD1 – mediator of DNA damage checkpoint 1; TREX1 – three prime repair exonuclease 1. The ataxia-telangiectasia mutated (ATM) kinase signals the presence of DNA double-strand breaks in mammalian cells by phosphorylating proteins that initiate cell-cycle arrest, apoptosis, and DNA repair. The Mre11-Rad50-Nbs1 (MRN) complex acts as a double-strand break sensor for ATM and recruits ATM to broken DNA molecules [42]. Activated ATM phosphorylates its downstream cellular targets H2AFX and Chk2 as well as proteins directly involved in DNA repair: XRCC5, TREX1 and NFBD1. G22P1 and PRKDC are subunits of DNA activated protein kinase that can be induced by DNA damage to promote DNA end joining [43]. It also can attenuate CHK2 control of the damage checkpoint [44]. A – The portion of GO classification overlapping with network cluster. The GO classification tree depiction is the same as in Figure 5A. B – The network cluster overlapping with GO classification from Figure A. Highlighted proteins belong to the best overlapping GO group from molecular function classification – telomere capping (GO:0016233). The proteins selected by the blue line belong to the second best overlapping GO group from combined biological processes classification – double-strand break repair (GO:0006302). Gray links indicate DirectRegulation relation, violet links indicate Binding relation, and green arrows represent ProtModification relations.