Noise-robust algorithm for identifying functionally associated biclusters from gene expression data

Authors:
Jaegyoon Ahn;Youngmi Yoon;Sanghyun Park
Affiliations:
Computer Science Department, Yonsei University, South Korea;Division of Information Technology, Gachon University of Medicine and Science, South Korea;Computer Science Department, Yonsei University, South Korea
Venue:
Information Sciences: an International Journal
Year:
2011

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Abstract

Biclusters are subsets of genes that exhibit similar behavior over a set of conditions. A biclustering algorithm is a useful tool for uncovering groups of genes involved in the same cellular processes and groups of conditions under which these processes take place. In this paper, we propose a polynomial time algorithm to identify functionally highly correlated biclusters. Our algorithm identifies (1) gene sets that simultaneously exhibit additive, multiplicative, and combined patterns and allow high levels of noise, (2) multiple, possibly overlapped, and diverse gene sets, (3) biclusters that simultaneously exhibit negatively and positively correlated gene sets, and (4) gene sets for which the functional association is very high. We validate the level of functional association in our method by using the GO database, protein-protein interactions and KEGG pathways.