Title: A system biology approach for understanding the miRNA regulatory network in colon rectal cancer

Authors: Meeta Pradhan; Kshithija Nagulapalli; Lakenvia Ledford; Yogesh Pandit; Mathew Palakal

Addresses: School of Informatics & Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA ' School of Informatics & Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA ' Indiana University, Bloomington, IN, USA ' School of Informatics & Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA ' School of Informatics & Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA

Abstract: In this paper we present a systems biology approach to the understanding of the miRNA-regulatory network in colon rectal cancer. An initial set of significant genes in Colon Rectal Cancer (CRC) were obtained by mining relevant literature. An initial set of cancer-related miRNAs were obtained from three databases: miRBase, miRWalk, Targetscan and GEO microarray experiment. First principle methods were then used to generate the global miRNA-gene network. Significant miRNAs and associated transcription factors in the global miRNA-gene network were identified using topological and sub-graph analyses. Eleven novel miRNAs were identified and three of the novel miRNAs, hsa-miR-630, hsa-miR-100 and hsa-miR-99a, were further analysed to elucidate their role in CRC. The proposed methodology effectively made use of literature data and was able to show novel, significant miRNA-transcription associations in CRC.

Keywords: genes; topological features; transcription factors; sub-graph analysis; pathways; systems biology; miRNA regulatory networks; colon rectal cancer; colon cancer; data mining; bioinformatics.

DOI: 10.1504/IJDMB.2015.066332

International Journal of Data Mining and Bioinformatics, 2015 Vol.11 No.1, pp.1 - 30

Received: 11 May 2012
Accepted: 11 May 2012

Published online: 17 Dec 2014 *

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