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Bioinformatics Advance Access originally published online on January 29, 2009
Bioinformatics 2009 25(6):832-833; doi:10.1093/bioinformatics/btp059
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

CORNA: testing gene lists for regulation by microRNAs

X. Wu * and M Watson

Bioinformatics Group, Institute for Animal Health, Compton, RG20 7NN, UK

*To whom correspondence should be addressed.


  Abstract

Motivation: With the increasing use of post-genomics techniques to examine a wide variety of biological systems in laboratories throughout the world, scientists are often presented with lists of genes that they must make sense of. A consistently challenging problem is that of defining co-regulated genes within those gene lists. In recent years, microRNAs have emerged as a mechanism for regulating several cellular processes. In this article, we report on how gene lists and microRNA targets data may be integrated to test for significant associations between gene lists and microRNAs.

Results: We discuss CORNA, a package written in R and released under the GNU GPL, which allows users to test gene lists for significant microRNA–target associations using one of three separate statistical tests, to link microRNA targets to functional annotation and to visualize quantitative data associated with those data.

Availability: CORNA is available as an R package from http://corna.sf.net

Contact: xikun.wu{at}bbsrc.ac.uk

Associate Editor: Ivo Hofacker

Received on November 19, 2008; revised on January 6, 2009; accepted on January 25, 2009

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A. V. Antonov, S. Dietmann, P. Wong, D. Lutter, and H. W. Mewes
GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W323 - W328.
[Abstract] [Full Text] [PDF]


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