Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data. (3rd October 2005)

• Record Type: Journal Article
• Authors: Joshi, Trupti; Chen, Yu; Alexandrov, Nickolai N.; Xu, Dong
• Is Part Of: International journal of bioinformatics research and applications. Volume 1:Number 3(2005)
• Page Start: 335
• Page End: 350
• Publication Date: 2005-10-03
• Subjects: cellular function prediction -- microarray gene expression profiles -- protein-protein interactions -- high-throughput data -- Arabidopsis thaliana -- biological pathways -- bioinformatics -- gene ontology -- protein function; Bioinformatics -- Periodicals; 570.285
• Languages: English
• ISSNs: 1744-5485

Abstract

Determination of protein function and biological pathway is one of the most challenging problems in the post-genomic era. To address this challenge, we have developed a new integrated probabilistic method for cellular function prediction using microarray gene expression profiles, in conjunction with predicted protein-protein interactions and annotations of known proteins. Our approach is based on a novel assessment for the relationship between correlation of two genes' expression profiles and their functional relationship in terms of the Gene Ontology (GO) hierarchy. We applied the method for function prediction of hypothetical genes in Arabidopsis. We have also extended our method using Dijkstra's algorithm to identify the components and topology of signaling pathway of phosphatidic acid as a second messenger in Arabidopsis.