©1996-2009
All Rights Reserved. Online Journal of Bioinformatics . You may not store these pages in
any form except
for your own personal use. All other usage or distribution is illegal
under
international copyright treaties. Permission to use any of these pages
in any
other way besides the before mentioned must be gained in
writing from the
publisher. This article is exclusively copyrighted in its entirety to
OJB
publications. This article may be copied once but may not be,
reproduced or re-transmitted without the express
permission of
the editors. This journal satisfies the
refereeing requirements (DEST) for the Higher Education Research Data
Collection (Australia). Linking:To link to this page or any pages
linking to this
page you must link directly to this page only here rather than put up
your own
page.
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.