TY - GEN
T1 - Exhaustive search of maximal biclusters in gene expression data
AU - Okada, Yoshifumi
AU - Fujibuchi, Wataru
AU - Horton, Paul
PY - 2007/12/1
Y1 - 2007/12/1
N2 - Recently, several methods have been suggested to discover biclusters from gene expression data matrices, where a bicluster is defined as a subset of genes that exhibit a highly correlated expression pattern over a subset of conditions. Most of them produce sub-optimal biclusters with greedy or stochastic approach. In contrast, we propose a new biclustering method, BiModule, that exhaustively searches biclusters in a realistic time based on a closed itemset mining algorithm. Comparative experiments to salient biclustering methods are performed to test the validity of biclusters extracted by BiModule using synthetic data and real expression data. We show that BiModule provides high performance compared to the other methods in extracting artificially-embedded modules as well as modules strongly related to GO annotations and protein-protein interactions.
AB - Recently, several methods have been suggested to discover biclusters from gene expression data matrices, where a bicluster is defined as a subset of genes that exhibit a highly correlated expression pattern over a subset of conditions. Most of them produce sub-optimal biclusters with greedy or stochastic approach. In contrast, we propose a new biclustering method, BiModule, that exhaustively searches biclusters in a realistic time based on a closed itemset mining algorithm. Comparative experiments to salient biclustering methods are performed to test the validity of biclusters extracted by BiModule using synthetic data and real expression data. We show that BiModule provides high performance compared to the other methods in extracting artificially-embedded modules as well as modules strongly related to GO annotations and protein-protein interactions.
UR - http://www.scopus.com/inward/record.url?scp=84888338452&partnerID=8YFLogxK
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M3 - Conference contribution
AN - SCOPUS:84888338452
SN - 9789889867140
T3 - Lecture Notes in Engineering and Computer Science
SP - 307
EP - 312
BT - IMECS 2007 - International MultiConference of Engineers and Computer Scientists 2007
T2 - International MultiConference of Engineers and Computer Scientists 2007, IMECS 2007
Y2 - 21 March 2007 through 23 March 2007
ER -