title: New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana.
abstract: Identifying sets of genes that are specifically expressed in certain tissues or in response to an environmental stimulus is useful for designing reporter constructs, generating gene expression markers, or for understanding gene regulatory networks. We have developed an easy-to-use online tool for defining a desired expression profile (a modification of our Expression Angler program), which can then be used to identify genes exhibiting patterns of expression that match this profile as closely as possible. Further, we have developed another online tool, Cistome, for predicting or exploring cis-elements in the promoters of sets of co-expressed genes identified by such a method, or by other methods. We present two use cases for these tools, which are freely available on the Bio-Analytic Resource at http://BAR.utoronto.ca.
authors.affiliation: Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada.
authors.forename: Ryan S
authors.initials: RS
authors.lastname: Austin
authors.affiliation: Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada.
authors.forename: Shu
authors.initials: S
authors.lastname: Hiu
authors.affiliation: Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada.
authors.forename: Jamie
authors.initials: J
authors.lastname: Waese
authors.affiliation: Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada.
authors.forename: Matthew
authors.initials: M
authors.lastname: Ierullo
authors.affiliation: Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada.
authors.forename: Asher
authors.initials: A
authors.lastname: Pasha
authors.affiliation: Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada.
authors.forename: Ting Ting
authors.initials: TT
authors.lastname: Wang
authors.affiliation: Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada.
authors.forename: Jim
authors.initials: J
authors.lastname: Fan
authors.affiliation: Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada.
authors.forename: Curtis
authors.initials: C
authors.lastname: Foong
authors.affiliation: Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada.
authors.forename: Robert
authors.initials: R
authors.lastname: Breit
authors.affiliation: Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada.
authors.forename: Darrell
authors.initials: D
authors.lastname: Desveaux
authors.affiliation: Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada.
authors.forename: Alan
authors.initials: A
authors.lastname: Moses
authors.affiliation: Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Provart
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D057225:Data Mining; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D011401:Promoter Regions, Genetic / Q000235:genetics; D012984:Software
keywords: 
  Arabidopsis thaliana
  ; cis-element prediction; coexpression analysis; gene expression markers; promoter analysis; reporter constructs; technical advance