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Online Journal of Bioinformatics ©
Volume 10 (2): 280-296, 2009.
Analysis of clustered microRNA in biological pathways
Sushmita Mookherjee1, Mithun Sinha2, Saikat Mukhopadhyay3,
Nitai P. Bhattacharyya2,3 and P. K. Mohanty4
1Centre for Applied Mathematics and Computational Science, 2Structural Genomics Section, 3Crystallography and Molecular Biology Division, 4Theoretical Condensed Matter Physics Division, Saha Institute of Nuclear Physics,1/AF Bidhan Nagar, Kolkata, 700064 India.
Mookherjee S, Sinha M, Mukhopadhyay S, Bhattacharyya NP, Mohanty PK., Analysis of clustered microRNA in biological pathways, Online J Bioinformatics, 10 (2): 280-296, 2009. A novel group of small non-coding RNA, known as microRNA (miRNA) is predicted to regulate as high as 90% of the coding genes in human. The diversity and abundance of miRNA targets offer an enormous level of combinatorial possibilities and suggest that miRNAs and their targets form a complex regulatory network. In the present study, we analyzed 711 miRNAs and their 34, 525 predicted targets in the miRBase (http://microrna.sanger.ac.uk/, version 10), which generate a complex bipartite network having numerous numbers of genes forming the hub. We further construct a miRNA co-target network by linking every pair of miRNAs which co-target at least one gene. The weight of the link, which is taken to be the number of co-targets of the pair of miRNAs vary widely, and we could erase several links while keeping the relevant features of the network intact. The largest connected sub-graph, thus obtained, contains 479 miRNAs. We further analyze this sub-graph to obtain 70 small clusters containing total 330 miRNAs of 479. We identified the biological pathways where the co-targeted genes in the clusters are significantly over represented in comparison to that obtained with that are not co-targeted by the miRNAs in the cluster using PANTHER (http://www.pantherdb.org/genes/). We propose that instead of single miRNA, clusters of miRNA that co-targets the genes are important for the regulation of miRNA in specific biological pathway.
Key words : Clustered microRNA; networks; pathways.