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OJBTM
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.
ABSTRACT
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.