title: Boosting AthaMap Database Content with Data from Protein Binding Microarrays.
abstract: The AthaMap database generates a map of predicted transcription factor binding sites (TFBS) and small RNA target sites for the whole Arabidopsis thaliana genome. With the advent of protein binding microarrays (PBM), the number of known TFBS for A. thaliana transcription factors (TFs) has increased dramatically. Using 113 positional weight matrices (PWMs) generated from a single PBM study and representing a total number of 68 different TFs, the number of predicted TFBS in AthaMap was now increased by about 3.8 × 10(7) to 4.9 × 10(7). The number of TFs with PWM-predicted TFBS annotated in AthaMap has increased to 126, representing a total of 29 TF families and newly including ARF, AT-Hook, YABBY, LOB/AS2 and SRS. Furthermore, links from all Arabidopsis TFs and genes to the newly established Arabidopsis Information Portal (AIP) have been implemented. With this qualitative and quantitative update, the improved AthaMap increases its value as a resource for the analysis of A. thaliana gene expression regulation at www.athamap.de.
authors.affiliation: Technische Universität Braunschweig, Institut für Genetik, Spielmannstr. 7, D-38106 Braunschweig, Germany r.hehl@tu-bs.de.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Hehl
authors.affiliation: Technische Universität Braunschweig, Institut für Genetik, Spielmannstr. 7, D-38106 Braunschweig, Germany.
authors.forename: Leo
authors.initials: L
authors.lastname: Norval
authors.affiliation: Technische Universität Braunschweig, Institut für Genetik, Spielmannstr. 7, D-38106 Braunschweig, Germany.
authors.forename: Artyom
authors.initials: A
authors.lastname: Romanov
authors.affiliation: Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Erwin-Baur-Str. 27, D-06484 Quedlinburg, Germany.
authors.forename: Lorenz
authors.initials: L
authors.lastname: Bülow
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D019295:Computational Biology; D030541:Databases, Genetic; D040081:Protein Array Analysis; D011485:Protein Binding; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D014157:Transcription Factors
keywords: Arabidopsis thaliana; AthaMap; Database; Small RNAs; Transcription factors