title: IT3F: a web-based tool for functional analysis of transcription factors in plants.
abstract: A web-based tool, the Interspecies Transcription Factor Function Finder (IT3F), has been developed to display both evolutionary gene relationships and expression data for plant transcription factors, focussing primarily on the R2R3MYB gene subfamily for proof of concept. The graphical display of information allows users to make direct comparisons between structurally related genes and to identify those genes that are potentially orthologous, thereby assisting with their understanding of gene function. A key feature of the website is the provision of an interrogative phylogenetic tree that allows submission of new sequences corresponding to a transcription factor family or subfamily and maps their relative positions to the products of other genes on an 'existing' tree containing proteins encoded by Arabidopsis and rice genes, along with key proteins encoded by genes from other species that have been characterised functionally. In addition, a feature to select clusters of related sequences has been developed so that more detailed phylogenetic analysis can be performed to highlight potential orthologous and paralogous genes within related clusters. Arabidopsis genes that reside on duplicated regions of the genome are indicated on the tree, providing further information for interpreting gene function. An additional feature of the website allows a selected number of key Arabidopsis and rice microarray experiments to be visualised alongside the tree as a tabulated heat map of expression intensity values. Through this display, it is possible to observe relative expression levels across a whole gene family and the extent to which the expression of closely related genes within subgroups has altered since their ancestral divergence. The website is available at http://jicbio.nbi.ac.uk/IT3F/.
authors.affiliation: Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK. Paul.Baioley@bbsrc.ac.uk
authors.forename: Paul C
authors.initials: PC
authors.lastname: Bailey
authors.forename: Jo
authors.initials: J
authors.lastname: Dicks
authors.forename: Trevor L
authors.initials: TL
authors.lastname: Wang
authors.forename: Cathie
authors.initials: C
authors.lastname: Martin
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D029681:Arabidopsis Proteins / Q000145:classification / Q000235:genetics / Q000502:physiology; D019295:Computational Biology / Q000379:methods; D020407:Internet; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000502:physiology; D017386:Sequence Homology, Amino Acid; D012984:Software; D014157:Transcription Factors / Q000145:classification / Q000235:genetics* / Q000502:physiology
chemical_list: D029681:Arabidopsis Proteins; C482738:BOTRYTIS SUSCEPTIBLE1 protein, Arabidopsis; D010940:Plant Proteins; D014157:Transcription Factors