title: RARTF: database and tools for complete sets of Arabidopsis transcription factors.
abstract: More than 5% of all genes in the Arabidopsis thaliana genome have been assumed to code for transcription factors. However, it has been difficult to accurately identify them. To construct proper sets of transcription factors, we used PSI-BLAST and InterProScan, and also checked several families manually. Especially to determine major Arabidopsis transcription factors (MYB, AP2/EREBP, bHLH, NAC, MADS, bZIP, WRKY), we compared the PSI-BLAST search results with those in recent reports. Finally, we identified 1968 proteins as transcription factors (7.4% of all Arabidopsis genes). We established a database named RARTF (RIKEN Arabidopsis Transcription Factor database, http://rarge.gsc.riken.jp/rartf/) based on the identified transcription factors. In RARTF, we provide information on the functional motif of transcription factors, full-length cDNAs, alternative pre-mRNA splicing events and Ac/Ds transposon-tagged mutants. We also provide expression profiles of 400 transcription factor genes in six experiments. We will report expression profiles of all transcription factor genes in various plant tissues under various stress and hormone conditions in the near future.
authors.affiliation: Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Japan. k_iida@nagahama-i-bio-ac.jp
authors.forename: Kei
authors.initials: K
authors.lastname: Iida
authors.forename: Motoaki
authors.initials: M
authors.lastname: Seki
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Sakurai
authors.forename: Masakazu
authors.initials: M
authors.lastname: Satou
authors.forename: Kenji
authors.initials: K
authors.lastname: Akiyama
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Toyoda
authors.forename: Akihiko
authors.initials: A
authors.lastname: Konagaya
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D018076:DNA, Complementary / Q000235:genetics / Q000378:metabolism; D030561:Databases, Nucleic Acid; D018745:Genome, Plant; D008969:Molecular Sequence Data; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D018076:DNA, Complementary; D014157:Transcription Factors