title: Uncovering mechanisms of transcriptional regulations by systematic mining of cis regulatory elements with gene expression profiles.
abstract: BACKGROUND
  Contrary to the traditional biology approach, where the expression patterns of a handful of genes are studied at a time, microarray experiments enable biologists to study the expression patterns of many genes simultaneously from gene expression profile data and decipher the underlying hidden biological mechanism from the observed gene expression changes. While the statistical significance of the gene expression data can be deduced by various methods, the biological interpretation of the data presents a challenge.
  
  
  RESULTS
  A method, called CisTransMine, is proposed to help infer the underlying biological mechanisms for the observed gene expression changes in microarray experiments. Specifically, this method will predict potential cis-regulatory elements in promoter regions which could regulate gene expression changes. This approach builds on the MotifADE method published in 2004 and extends it with two modifications: up-regulated genes and down-regulated genes are tested separately and in addition, tests have been implemented to identify combinations of transcription factors that work synergistically. The method has been applied to a genome wide expression dataset intended to study myogenesis in a mouse C2C12 cell differentiation model. The results shown here both confirm the prior biological knowledge and facilitate the discovery of new biological insights.
  
  
  CONCLUSIONS
  The results validate that the CisTransMine approach is a robust method to uncover the hidden transcriptional regulatory mechanisms that can facilitate the discovery of mechanisms of transcriptional regulation.
authors.affiliation: Developmental and Molecular Pathways, Novartis Institutes For Biomedical Research Inc, 250 Massachusetts Avenue, Cambridge, MA 02139, USA. Qicheng.Ma@novartis.com
authors.forename: Qicheng
authors.initials: Q
authors.lastname: Ma
authors.forename: Gung-Wei
authors.initials: GW
authors.lastname: Chirn
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Szustakowski
authors.forename: Adel
authors.initials: A
authors.lastname: Bakhtiarova
authors.forename: Penelope A
authors.initials: PA
authors.lastname: Kosinski
authors.forename: Daniel
authors.initials: D
authors.lastname: Kemp
authors.forename: Nanguneri
authors.initials: N
authors.lastname: Nirmala