A novel biological pathway expansion method based on the knowl-edge of protein-protein interactions
Received date: 2013-09-23
Revised date: 2013-12-04
Online published: 2014-03-26
Supported by
protein?protein interaction|Gene Ontology|enrichment analysis|pathway attribution|prediction
Biological pathways have been widely used in gene function studies; however, the current knowledge for biological pathways is per se incomplete and has to be further expanded. Bioinformatics prediction provides us a cheap but effective way for pathway expansion. Here, we proposed a novel method for biological pathway prediction, by intergrating prior knowledge of protein?protein interactions and Gene Ontology (GO) database. First, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways to which the interacting neighbors of a targe gene (at the level of protein?protein interaction) belong were chosen as the candidate pathways. Then, the pathways to which the target gene belong were determined by testing whether the genes in the candidate pathways were enriched in the GO terms to which the target gene were annotated. The protein?protein interaction data obtained from the Human Protein Reference Database (HPRD) and Biological General Repository for Interaction Datasets (BioGRID) were respectively used to predict the pathway attribution(s) of the target gene. The results demanstrated that both the average accuracy (the ratio of the correctly predicted pathways to the totally pathways to which all the target genes were annotated) and the relative accuracy (of the genes with at least one annotated pathway being successful predicted, the percentage of the genes with all the annotated pathways being correctly predicted) for pathway predictions were increased with the number of the interacting neighbours. When the number of interacting neighbours reached 22, the average accuracy was 96.2% (HPRD) and 96.3% (BioGRID), respectively, and the relative accuracy was 93.3% (HPRD) and 84.1% (BioGRID), respectively. Further validation analysis of 89 genes whose pathway knowledge was updated in a new database release indicated that 50 genes were correctly predicted for at least one updated pathway, and 43 genes were accurately predicted for all the updated pathways, giving an estimate of the relative accuracy of 86.0%. These results demonstrated that the proposed approach was a reliable and effective method for pathway expansion.
Xiaolei Zhao, Xiaoyu Zuo, Jiheng Qin, Yan Liang, Naizun Zhang, Yizhao Luan, Shaoqi Rao . A novel biological pathway expansion method based on the knowl-edge of protein-protein interactions[J]. Hereditas(Beijing), 2014 , 36(4) : 387 -394 . DOI: 10.3724/SP.J.1005.2014.0387
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