RN + : A Novel Biclustering Algorithm for Analysis of Gene Expression Data Using Protein–Protein Interaction Network

Abstract

Abstract

Biclustering is a process of finding groups of genes that behave similarly under a subset of conditions. In this article, we propose an efficient biclustering algorithm, namely RN⁺, to identify biologically meaningful biclusters in gene expression data. The RN⁺ algorithm finds biologically meaningful biclusters through a novel gene filtering using protein–protein interaction network, gene searching, gene grouping, and queuing process. It also efficiently removes duplicate biclusters. We tested the proposed RN⁺ on five real microarray datasets, and compared its performance with seven competitive biclustering algorithms. The experimental results show that RN⁺ efficiently finds functionally enriched and biologically meaningful biclusters for large gene expression datasets, and outperforms the other tested biclustering algorithms on real datasets.