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Open Access Methodology article

Incorporating the type and direction information in predicting novel regulatory interactions between HIV-1 and human proteins using a biclustering approach

Anirban Mukhopadhyay1, Sumanta Ray2* and Ujjwal Maulik3*

Author Affiliations

1 Department of Computer Science and Engineering, University of Kalyani, Kalyani-741235, West Bengal, India

2 Department of Computer Science and Engineering, Aliah University, Kolkata-700091, West Bengal, India

3 Department of Computer Science and Engineering, Jadavpur University, Kolkata-700032, West Bengal, India

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BMC Bioinformatics 2014, 15:26  doi:10.1186/1471-2105-15-26

Published: 24 January 2014

Abstract

Background

Discovering novel interactions between HIV-1 and human proteins would greatly contribute to different areas of HIV research. Identification of such interactions leads to a greater insight into drug target prediction. Some recent studies have been conducted for computational prediction of new interactions based on the experimentally validated information stored in a HIV-1-human protein-protein interaction database. However, these techniques do not predict any regulatory mechanism between HIV-1 and human proteins by considering interaction types and direction of regulation of interactions.

Results

Here we present an association rule mining technique based on biclustering for discovering a set of rules among human and HIV-1 proteins using the publicly available HIV-1-human PPI database. These rules are subsequently utilized to predict some novel interactions among HIV-1 and human proteins. For prediction purpose both the interaction types and direction of regulation of interactions, (i.e., virus-to-host or host-to-virus) are considered here to provide important additional information about the regulation pattern of interactions. We have also studied the biclusters and analyzed the significant GO terms and KEGG pathways in which the human proteins of the biclusters participate. Moreover the predicted rules have also been analyzed to discover regulatory relationship between some human proteins in course of HIV-1 infection. Some experimental evidences of our predicted interactions have been found by searching the recent literatures in PUBMED. We have also highlighted some human proteins that are likely to act against the HIV-1 attack.

Conclusions

We pose the problem of identifying new regulatory interactions between HIV-1 and human proteins based on the existing PPI database as an association rule mining problem based on biclustering algorithm. We discover some novel regulatory interactions between HIV-1 and human proteins. Significant number of predicted interactions has been found to be supported by recent literature.