title: Extracting regulatory modules from gene expression data by sequential pattern mining.
abstract: 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.affiliation: Seoul National University Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea.
authors.forename: Mingoo
authors.initials: M
authors.lastname: Kim
authors.forename: Hyunjung
authors.initials: H
authors.lastname: Shin
authors.forename: Tae
authors.initials: T
authors.lastname: Su Chung
authors.forename: Je-Gun
authors.initials: JG
authors.lastname: Joung
authors.forename: Ju Han
authors.initials: JH
authors.lastname: Kim
mesh_terms: D000465:Algorithms; D057225:Data Mining; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D020411:Oligonucleotide Array Sequence Analysis; D012441:Saccharomyces cerevisiae / Q000235:genetics