title: A predicted protein-protein interaction network of the filamentous fungus Neurospora crassa.
abstract: The filamentous fungus Neurospora crassa is a leading model organism for circadian clock studies. Computational identification of a protein-protein interaction (PPI) network (also known as an interactome) in N. crassa can provide new insights into the cellular functions of proteins. Using two well-established bioinformatics methods (the interolog method and the domain interaction-based method), we predicted 27,588 PPIs among 3006 N. crassa proteins. To the best of our knowledge, this is the first identified interactome for N. crassa, although it remains problematic because of incomplete interactions and false positives. In particular, the established PPI network has provided clues to further decipher the molecular mechanism of circadian rhythmicity. For instance, we found that clock-controlled genes (ccgs) are more likely to act as bottlenecks in the established PPI network. We also identified an important module related to circadian oscillators, and some functional unknown proteins in this module may serve as potential candidates for new oscillators. Finally, all predicted PPIs were compiled into a user-friendly database server (NCPI), which is freely available at .
authors.affiliation: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
authors.forename: Ting-You
authors.initials: TY
authors.lastname: Wang
authors.forename: Fei
authors.initials: F
authors.lastname: He
authors.forename: Qi-Wen
authors.initials: QW
authors.lastname: Hu
authors.forename: Ziding
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D057906:Circadian Clocks / Q000502:physiology; D002940:Circadian Rhythm / Q000502:physiology; D030562:Databases, Protein; D005656:Fungal Proteins / Q000378:metabolism*; D020407:Internet; D009492:Neurospora crassa / Q000378:metabolism* / Q000502:physiology; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D015203:Reproducibility of Results; D015398:Signal Transduction
chemical_list: D005656:Fungal Proteins