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Prediction and characterization of protein-protein interaction networks in swine

Fen Wang1, Min Liu1, Baoxing Song2, Dengyun Li2, Huimin Pei3, Yang Guo1, Jingfei Huang4* and Deli Zhang2*

Author Affiliations

1 College of Life Science, Center for Bioinformatics, Northwest A&F University, Yangling, Shaanxi 712100, China

2 College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China

3 College of forestry, Northwest A&F University, Yangling, Shaanxi 712100, China

4 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, P.R. China

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Proteome Science 2012, 10:2  doi:10.1186/1477-5956-10-2

Published: 10 January 2012

Abstract

Background

Studying the large-scale protein-protein interaction (PPI) network is important in understanding biological processes. The current research presents the first PPI map of swine, which aims to give new insights into understanding their biological processes.

Results

We used three methods, Interolog-based prediction of porcine PPI network, domain-motif interactions from structural topology-based prediction of porcine PPI network and motif-motif interactions from structural topology-based prediction of porcine PPI network, to predict porcine protein interactions among 25,767 porcine proteins. We predicted 20,213, 331,484, and 218,705 porcine PPIs respectively, merged the three results into 567,441 PPIs, constructed four PPI networks, and analyzed the topological properties of the porcine PPI networks. Our predictions were validated with Pfam domain annotations and GO annotations. Averages of 70, 10,495, and 863 interactions were related to the Pfam domain-interacting pairs in iPfam database. For comparison, randomized networks were generated, and averages of only 4.24, 66.79, and 44.26 interactions were associated with Pfam domain-interacting pairs in iPfam database. In GO annotations, we found 52.68%, 75.54%, 27.20% of the predicted PPIs sharing GO terms respectively. However, the number of PPI pairs sharing GO terms in the 10,000 randomized networks reached 52.68%, 75.54%, 27.20% is 0. Finally, we determined the accuracy and precision of the methods. The methods yielded accuracies of 0.92, 0.53, and 0.50 at precisions of about 0.93, 0.74, and 0.75, respectively.

Conclusion

The results reveal that the predicted PPI networks are considerably reliable. The present research is an important pioneering work on protein function research. The porcine PPI data set, the confidence score of each interaction and a list of related data are available at (http://pppid.biositemap.com webcite/).

Keywords:
protein-protein interaction network; Interolog; D-MIST; M-MIST topological properties; Pfam domain annotations; GO annotations