ppdb: plant promoter database version 3.0

被引：53

作者：

Hieno, Ayaka ^{[1
]}

Naznin, Hushna Ara ^{[1
]}

Hyakumachi, Mitsuro ^{[1
,2
]}

Sakurai, Tetsuya ^{[3
]}

Tokizawa, Mututomo ^{[1
]}

Koyama, Hiroyuki ^{[1
,2
]}

Sato, Naoki ^{[4
]}

Nishiyama, Tomoaki ^{[5
]}

Hasebe, Mitsuyasu ^{[6
,7
]}

Zimmer, Andreas D. ^{[8
]}

Lang, Daniel ^{[8
]}

Reski, Ralf ^{[8
]}

Rensing, Stefan A. ^{[9
]}

Obokata, Junichi ^{[10
]}

Yamamoto, Yoshiharu Y. ^{[1
,2
,3
]}

机构：

[1] Gifu Univ, United Grad Sch Agr Sci, Gifu 5011193, Japan

[2] Gifu Univ, Fac Appl Biol Sci, Gifu 5011193, Japan

[3] RIKEN Yokohama Inst, Ctr Sustainable Resource Sci, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan

[4] Univ Tokyo, Grad Sch Arts & Sci, Meguro Ku, Tokyo 1538902, Japan

[5] Kanazawa Univ, Adv Sci Res Ctr, Kanazawa, Ishikawa 9200934, Japan

[6] Natl Inst Basic Biol, Okazaki, Aichi 4448585, Japan

[7] Grad Univ Adv Studies, Sch Life Sci, Dept Basic Biol, Okazaki, Aichi 4448585, Japan

[8] Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany

[9] Univ Marburg, Fac Biol, D-35043 Marburg, Germany

[10] Kyoto Prefectural Univ, Grad Sch Environm Life Sci, Sakyo Ku, Kyoto 6068522, Japan

来源：

NUCLEIC ACIDS RESEARCH | 2014年 / 42卷 / D1期

基金：

日本科学技术振兴机构;

关键词：

FUNCTIONAL ANNOTATION; CDNA-CLONES; GENOME; COLLECTION; INSIGHTS; ELEMENTS; RICE;

D O I：

10.1093/nar/gkt1027

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 similar to 200-fold increase in TSS data compared with version 1.0. This results in a much higher coverage of similar to 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.

引用

页码：D1188 / D1192

页数：5

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