Genome-wide protein-protein interactions and protein function exploration in cyanobacteria.
Genome-wide network analysis is well implemented to study proteins of unknown function. Here, we effectively explored protein functions and the biological mechanism based on inferred high confident protein-protein interaction (PPI) network in cyanobacteria. We integrated data from seven different sources and predicted 1,997 PPIs, which were evaluated by experiments in molecular mechanism, text mining of literatures in proved direct/indirect evidences, and "interologs" in conservation. Combined the predicted PPIs with known PPIs, we obtained 4,715 no-redundant PPIs (involving 3,231 proteins covering over 90% of genome) to generate the PPI network. Based on the PPI network, terms in Gene ontology (GO) were assigned to function-unknown proteins. Functional modules were identified by dissecting the PPI network into sub-networks and analyzing pathway enrichment, with which we investigated novel function of underlying proteins in protein complexes and pathways. Examples of photosynthesis and DNA repair indicate that the network approach is a powerful tool in protein function analysis. Overall, this systems biology approach provides a new insight into posterior functional analysis of PPIs in cyanobacteria.
Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.
Qi
Q
Lv
College of Life and Environment Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China.
Weimin
W
Ma
Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.
Hui
H
Liu
Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.
Jiang
J
Li
Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.
Huan
H
Wang
College of Life and Environment Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China.
Fang
F
Lu
Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.
Chen
C
Zhao
Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.|The institute of plant physiology and ecology, Shanghai Institutes for Biological Sciences, Chinese Acedamy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
Tieliu
T
Shi
D000458:Cyanobacteria / Q000235:genetics* / Q000378:metabolism; D016680:Genome, Bacterial; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps / Q000235:genetics*; D011506:Proteins / Q000235:genetics* / Q000378:metabolism; D049490:Systems Biology
D011506:Proteins