Extracting Biological Significant Subnetworks from Protein-Protein Interactions Induced by Differentially Expressed Genes of HIV-1 Vpr Variants | IGI Global Scientific Publishing
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Extracting Biological Significant Subnetworks from Protein-Protein Interactions Induced by Differentially Expressed Genes of HIV-1 Vpr Variants

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

Bandana Barman, Anirban Mukhopadhyay
Copyright: © 2015 |Volume: 4 |Issue: 4 |Pages: 17
ISSN: 2160-9772|EISSN: 2160-9799|EISBN13: 9781466680388|DOI: 10.4018/IJSDA.2015100103
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MLA

Barman, Bandana, and Anirban Mukhopadhyay. "Extracting Biological Significant Subnetworks from Protein-Protein Interactions Induced by Differentially Expressed Genes of HIV-1 Vpr Variants." IJSDA vol.4, no.4 2015: pp.35-51. https://doi.org/10.4018/IJSDA.2015100103

APA

Barman, B. & Mukhopadhyay, A. (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), 4(4), 35-51. https://doi.org/10.4018/IJSDA.2015100103

Chicago

Barman, Bandana, and Anirban Mukhopadhyay. "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) 4, no.4: 35-51. https://doi.org/10.4018/IJSDA.2015100103

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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.

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