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Nucleic Acids Research Advance Access published online on May 6, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp294
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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.

Web Server Issue

MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression

Seungyoon Nam1, Meng Li1, Kwangmin Choi2, Curtis Balch1,3, Sun Kim2,* and Kenneth P. Nephew1,3,*

1Medical Sciences Program, Indiana University School of Medicine, 2Bioinformatics Program, School of Informatics, Indiana University, Bloomington and 3Indiana University Simon Cancer Center, Indianapolis, IN, USA

*To whom correspondence should be addressed. Tel: +1 812 856 3009; Fax: +1 812 856 4764; Email: sun.kim{at}acm.org Correspondence may also be addressed to Kenneth P. Nephew. Tel: +1 812 855 9445; Fax: +1 812 855 4436; Email: knephew{at}indiana.edu

Received March 4, 2009. Revised April 11, 2009. Accepted April 14, 2009.

MicroRNAs (miRNAs) are small (19–24 nt), nonprotein-coding nucleic acids that regulate specific ‘target’ gene products via hybridization to mRNA transcripts, resulting in translational blockade or transcript degradation. Although miRNAs have been implicated in numerous developmental and adult diseases, their specific impact on biological pathways and cellular phenotypes, in addition to miRNA gene promoter regulation, remain largely unknown. To improve and facilitate research of miRNA functions and regulation, we have developed MMIA (microRNA and mRNA integrated analysis), a versatile and user-friendly web server. By incorporating three commonly used and accurate miRNA prediction algorithms, TargetScan, PITA and PicTar, MMIA integrates miRNA and mRNA expression data with predicted miRNA target information for analyzing miRNA-associated phenotypes and biological functions by gene set analysis, in addition to analysis of miRNA primary transcript gene promoters. To assign biological relevance to the integrated miRNA/mRNA profiles, MMIA uses exhaustive human genome coverage, including classification into various disease-associated genes as well as conventional canonical pathways and Gene Ontology. In summary, this novel web server (cancer.informatics.indiana.edu/mmia) will provide life science researchers with a valuable tool for the study of the biological (and pathological) causes and effects of the expression of this class of interesting protein regulators.


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