InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic ge

Background: Although many genomic features have been used in the prediction of proteinprotein interactions (PPIs), frequently only one is used in a computational method. After realizing the limited power in the prediction using only one genomic feature, investigators are now moving toward integration. So far, there have been few integration studies for PPI prediction; one failed to yield appreciable improvement of prediction and the others did not conduct performance comparison. It remains unclear whether an integration of multiple genomic features can improve the PPI prediction and, if it can, how to integrate these features. Results: In this study, we first performed a systematic evaluation on the PPI prediction in Escherichia coli (E. coli) by four genomic context based methods: the phylogenetic profile method, the gene cluster method, the gene fusion method, and the gene neighbor method. The number of predicted PPIs and the average degree in the predicted PPI networks varied great...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao
• Keywords: BMCBI 2007, Genomic Features, PPI Prediction, Prediction