TY - JOUR
T1 - Ppdb
T2 - Plant promoter database version 3.0
AU - Hieno, Ayaka
AU - Naznin, Hushna Ara
AU - Hyakumachi, Mitsuro
AU - Sakurai, Tetsuya
AU - Tokizawa, Mututomo
AU - Koyama, Hiroyuki
AU - Sato, Naoki
AU - Nishiyama, Tomoaki
AU - Hasebe, Mitsuyasu
AU - Zimmer, Andreas D.
AU - Lang, Daniel
AU - Reski, Ralf
AU - Rensing, Stefan A.
AU - Obokata, Junichi
AU - Yamamoto, Yoshiharu Y.
PY - 2014/1/1
Y1 - 2014/1/1
N2 - ppdb (http://ppdb.agr.gifu-u.ac.jp) is a plant promoter database that provides information on transcription start sites (TSSs), core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA elements) and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Since the last report in this journal, the database has been updated in three areas to version 3.0. First, new genomes have been included in the database, and now ppdb provides information on Arabidopsis thaliana, rice, Physcomitrella patens and poplar. Second, new TSS tag data (34 million) from A. thaliana, determined by a high throughput sequencer, has been added to give a ∼200-fold increase in TSS data compared with version 1.0. This results in a much higher coverage of ∼27 000 A. thaliana genes and finer positioning of promoters even for genes with low expression levels. Third, microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles.
AB - ppdb (http://ppdb.agr.gifu-u.ac.jp) is a plant promoter database that provides information on transcription start sites (TSSs), core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA elements) and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Since the last report in this journal, the database has been updated in three areas to version 3.0. First, new genomes have been included in the database, and now ppdb provides information on Arabidopsis thaliana, rice, Physcomitrella patens and poplar. Second, new TSS tag data (34 million) from A. thaliana, determined by a high throughput sequencer, has been added to give a ∼200-fold increase in TSS data compared with version 1.0. This results in a much higher coverage of ∼27 000 A. thaliana genes and finer positioning of promoters even for genes with low expression levels. Third, microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles.
UR - http://www.scopus.com/inward/record.url?scp=84891757523&partnerID=8YFLogxK
U2 - 10.1093/nar/gkt1027
DO - 10.1093/nar/gkt1027
M3 - 学術論文
C2 - 24194597
AN - SCOPUS:84891757523
SN - 0305-1048
VL - 42
SP - D1188-D1192
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -