Journal Article

WebPARE: web-computing for inferring genetic or transcriptional interactions

Cheng-Long Chuang, Jia-Hong Wu, Chi-Sheng Cheng and Grace S. Shieh

in Bioinformatics

Volume 26, issue 4, pages 582-584
Published in print February 2010 | ISSN: 1367-4803
Published online December 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp684

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Summary: Inferring genetic or transcriptional interactions, when done successfully, may provide insights into biological processes or biochemical pathways of interest. Unfortunately, most computational algorithms require a certain level of programming expertise. To provide a simple web interface for users to infer interactions from time course gene expression data, we present WebPARE, which is based on the pattern recognition algorithm (PARE). For expression data, in which each type of interaction (e.g. activator target) and the corresponding paired gene expression pattern are significantly associated, PARE uses a non-linear score to classify gene pairs of interest into a few subclasses of various time lags. In each subclass, PARE learns the parameters in the decision score using known interactions from biological experiments or published literature. Subsequently, the trained algorithm predicts interactions of a similar nature. Previously, PARE was shown to infer two sets of interactions in yeast successfully. Moreover, several predicted genetic interactions coincided with existing pathways; this indicates the potential of PARE in predicting partial pathway components. Given a list of gene pairs or genes of interest and expression data, WebPARE invokes PARE and outputs predicted interactions and their networks in directed graphs.

Availability: A web-computing service WebPARE is publicly available at: http://www.stat.sinica.edu.tw/WebPARE

Contact: gshieh@stat.sinica.edu.tw

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1424 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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