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Extracting Biological Significant Subnetworks from Protein-Protein Interactions Induced by Differentially Expressed Genes of HIV-1 Vpr Variants

Author

Listed:
  • Bandana Barman

    (Department of Electronics and Communication Engineering, Kalyani Government Engineering College, Kalyani, India)

  • Anirban Mukhopadhyay

    (Department of Computer Science and Engineering, University of Kalyani, Kalyani, India)

Abstract

Identification of protein interaction network is very important to find the cell signaling pathway for a particular disease. The authors have found the differentially expressed genes between two sample groups of HIV-1. Samples are wild type HIV-1 Vpr and HIV-1 mutant Vpr. They did statistical t-test and found false discovery rate (FDR) to identify the genes increased in expression (up-regulated) or decreased in expression (down-regulated). In the test, the authors have computed q-values of test to identify minimum FDR which occurs. As a result they found 172 differentially expressed genes between their sample wild type HIV-1 Vpr and HIV-1 mutant Vpr, R80A. They found 68 up-regulated genes and 104 down-regulated genes. From the 172 differentially expressed genes the authors found protein-protein interaction network with string-db and then clustered (subnetworks) the PPI networks with cytoscape3.0. Lastly, the authors studied significance of subnetworks with performing gene ontology and also studied the KEGG pathway of those subnetworks.

Suggested Citation

  • Bandana Barman & Anirban Mukhopadhyay, 2015. "Extracting Biological Significant Subnetworks from Protein-Protein Interactions Induced by Differentially Expressed Genes of HIV-1 Vpr Variants," International Journal of System Dynamics Applications (IJSDA), IGI Global, vol. 4(4), pages 35-51, October.
    • Handle: RePEc:igg:jsda00:v:4:y:2015:i:4:p:35-51
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