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Inferring Quercetin mediated miRNA-TF-gene Regulatory circuit using meta-analysis of Gene expression data

Author Affiliations

  • 1Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam-785013, INDIA

Int. Res. J. Biological Sci., Volume 3, Issue (2), Pages 40-47, February,10 (2014)

Abstract

Both transcription factors (TFs) and microRNAs (miRNAs) are the key regulatory elements of genes at transcriptional and post-transcriptional levels. Though the mode of action these two elements vary significantly from each other, studies have shown that they can act upon genes in a combinatory network. In this study, we report an interaction map representing the combined regulatory effect of human TFs and miRNAs on the differentially expressed genes (DEGs) obtained from the meta-analysis of gene expression data based on quercetin mediated effect in human. Bioconductor packages were used with the help of R programming language to normalize and process three datasets: GSE7259, GSE15162 and GSE13899. Wilcoxon’s t-test was performed with the help of JAVA Multi-Experiment Viewer program (MeV) and the results revealed a total of 605 unique DEGs at p 0.05. Custom perl scripts searched 8 most common and frequent DEGs. BiNGO plug-in in Cytoscape analyzed the 8 DEGs and found 26 unique GO terms associated with 8 biological processes, 14 cellular components and 4 molecular functions. Bioinformatics tools identified 18 TFs for 7 DEGs except ATRX. The tools, miRanda and TargetScan identified 200 and 249 unique miRNAs targeting 8 DEGs and 9 TFs. The miRNA-TF-gene interaction map was constructed with the help of Cytoscape. The information obtained in this study provides insights into the dynamic characteristics of quercetin mediated miRNA-TF-gene circuit.

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