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Bioinformatics Advance Access originally published online on October 6, 2009
Bioinformatics 2009 25(23):3199-3201; doi:10.1093/bioinformatics/btp574
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ncRNAppi—a tool for identifying disease-related miRNA and siRNA targeting pathways

Ka-Lok Ng 1,*, Hsueh-Chuan Liu 2,* and Shan-Chih Lee 3

1 Department of Bioinformatics, Asia University, 500 Lioufeng Road, Wufeng Shiang, Taichung, Taiwan 41354, 2 Department of Computer Science, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, Taiwan 30013 and 3 School of Medical Imaging and Radiological Sciences, Chung Shan Medical University, Taichung, Taiwan 40201

* To whom correspondence should be addressed.


  Abstract

Summary: Currently, there are a number of databases which store microRNA (miRNA) information, and tools available which provide miRNA target prediction. In this article, we describe a novel web-based tool that integrate the miRNA-targeted mRNA data, protein–protein interactions (PPI) records, tissues, biochemical pathways, human disease and gene function information to establish a disease-related miRNA target pathway database. This database is unique in the sense that it links miRNA target genes with their PPI partners according to being tissue- and diseases-specific or both. The same approach is also applied to siRNA data. This database provides two types of searches: (i) tissue- and (ii) disease-specific miRNA (or siRNA) targeting pathways. The search allows one to identify tissue- or disease-specific miRNA (or siRNA) target gene's PPI partners two levels beyond.

Availability: The release version 1.0 is a freely accessible database available at http://ncrnappi.cs.nthu.edu.tw and http://ncRNAppi.bioinfo.asia.edu.tw/

Contact: ppiddi{at}gmail.com; o2snow{at}gmail.com

Associate Editor: Ivo Hofacker

Received on March 31, 2009; revised on September 21, 2009; accepted on September 26, 2009

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