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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, Onl J Bioinform, 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.
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