A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny.

ABSTRACT: Protein Domain Co-occurrence Network (DCN) is a biological network that has not been fully-studied. We analyzed the properties of the DCNs of H. sapiens, S. cerevisiae, C. elegans, D. melanogaster, and 15 plant genomes. These DCNs have the hallmark features of scale-free networks. We investigated the possibility of using DCNs to predict protein and domain functions. Based on our experiment conducted on 66 randomly selected proteins, the best of top 3 predictions made by our DCN-based aggregated neighbor-counting method achieved a semantic similarity score of 0.81 to the actual Gene Ontology terms of the proteins. Moreover, the top 3 predictions using neighbor-counting, χ(2), and a SVM-based method achieved an accuracy of 66%, 59%, and 61%, respectively, when used to predict specific Gene O

SUBMITTER: Wang Z 

PROVIDER: S-EPMC3063783 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature