seed-based biclustering of gene expression dataseed-based biclustering基因表达数据.pdfVIP

Seed-Based Biclustering of Gene Expression Data 1 2 1 Jiyuan An *, Alan Wee-Chung Liew , Colleen C. Nelson 1 Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia, 2 School of Information and Communication Technology, Gold Coast Campus, Griffith University, Queensland, Australia Abstract Background: Accumulated biological research outcomes show that biological functions do not depend on individual genes, but on complex gene networks. Microarray data are widely used to cluster genes according to their expression levels across experimental conditions. However, functionally related genes generally do not show coherent expression across all conditions since any given cellular process is active only under a subset of conditions. Biclustering finds gene clusters that have similar expression levels across a subset of conditions. This paper proposes a seed-based algorithm that identifies coherent genes in an exhaustive, but efficient manner. Methods: In order to find the biclusters in a gene expression dataset, we exhaustively select combinations of genes and conditions as seeds to create candidate bicluster tables. The tables have two columns (a) a gene set, and (b) the conditions on which the gene set have dissimilar expression levels to the seed. First, the genes with less than the maximum number of dissimilar conditions are identified and a table of these genes is created. Second, the rows that have the same dissimilar conditions are grouped together. Third, the table is sorted in ascending order based on the number of dissimilar conditions. Finally, beginning with the first row of the table, a test is run repeatedly to determine whether the cardinality of the gene set in the row is greater