BACKGROUND: Identifying a regulatory module (RM), a bi-set of co-regulated genes and co-regulating conditions (or samples), has been an important challenge in functional genomics and bioinformatics. Given a microarray gene-expression matrix, biclustering has been the most common method for extracting RMs. Among biclustering methods, order-preserving biclustering by a sequential pattern mining technique has native advantage over the conventional biclustering approaches since it preserves the order of genes (or conditions) according to the magnitude of the expression value. However, previous sequential pattern mining-based biclustering has several weak points in that they can easily be computationally intractable in the real-size of microarray data and sensitive to inherent noise in the expression value. RESULTS: In this paper, we propose a novel sequential pattern mining algorithm that is scalable in the size of microarray data and robust with respect to noise. When applied to the microarray data of yeast, the proposed algorithm successfully found long order-preserving patterns, which are biologically significant but cannot be found in randomly shuffled data. The resulting patterns are well enriched to known annotations and are consistent with known biological knowledge. Furthermore, RMs as well as inter-module relations were inferred from the biologically significant patterns. CONCLUSIONS: Our approach for identifying RMs could be valuable for systematically revealing the mechanism of gene regulation at a genome-wide level.
BACKGROUND: Identifying a regulatory module (RM), a bi-set of co-regulated genes and co-regulating conditions (or samples), has been an important challenge in functional genomics and bioinformatics. Given a microarray gene-expression matrix, biclustering has been the most common method for extracting RMs. Among biclustering methods, order-preserving biclustering by a sequential pattern mining technique has native advantage over the conventional biclustering approaches since it preserves the order of genes (or conditions) according to the magnitude of the expression value. However, previous sequential pattern mining-based biclustering has several weak points in that they can easily be computationally intractable in the real-size of microarray data and sensitive to inherent noise in the expression value. RESULTS: In this paper, we propose a novel sequential pattern mining algorithm that is scalable in the size of microarray data and robust with respect to noise. When applied to the microarray data of yeast, the proposed algorithm successfully found long order-preserving patterns, which are biologically significant but cannot be found in randomly shuffled data. The resulting patterns are well enriched to known annotations and are consistent with known biological knowledge. Furthermore, RMs as well as inter-module relations were inferred from the biologically significant patterns. CONCLUSIONS: Our approach for identifying RMs could be valuable for systematically revealing the mechanism of gene regulation at a genome-wide level.
Authors: Ziv Bar-Joseph; Georg K Gerber; Tong Ihn Lee; Nicola J Rinaldi; Jane Y Yoo; François Robert; D Benjamin Gordon; Ernest Fraenkel; Tommi S Jaakkola; Richard A Young; David K Gifford Journal: Nat Biotechnol Date: 2003-10-12 Impact factor: 54.908
Authors: Jodi E Hirschman; Rama Balakrishnan; Karen R Christie; Maria C Costanzo; Selina S Dwight; Stacia R Engel; Dianna G Fisk; Eurie L Hong; Michael S Livstone; Robert Nash; Julie Park; Rose Oughtred; Marek Skrzypek; Barry Starr; Chandra L Theesfeld; Jennifer Williams; Rey Andrada; Gail Binkley; Qing Dong; Christopher Lane; Stuart Miyasato; Anand Sethuraman; Mark Schroeder; Mayank K Thanawala; Shuai Weng; Kara Dolinski; David Botstein; J Michael Cherry Journal: Nucleic Acids Res Date: 2006-01-01 Impact factor: 16.971
Authors: Catherine A Ball; Ihab A B Awad; Janos Demeter; Jeremy Gollub; Joan M Hebert; Tina Hernandez-Boussard; Heng Jin; John C Matese; Michael Nitzberg; Farrell Wymore; Zachariah K Zachariah; Patrick O Brown; Gavin Sherlock Journal: Nucleic Acids Res Date: 2005-01-01 Impact factor: 16.971