ppdb: plant promoter database version 3.0
| Autor: | Mututomo Tokizawa, Mitsuyasu Hasebe, Naoki Sato, Mitsuro Hyakumachi, Junichi Obokata, Tetsuya Sakurai, Hiroyuki Koyama, Andreas Zimmer, Ralf Reski, Tomoaki Nishiyama, Ayaka Hieno, Stefan A. Rensing, Daniel Lang, Hushna Ara Naznin, Yoshiharu Y. Yamamoto |
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| Rok vydání: | 2013 |
| Předmět: |
TATA box
Arabidopsis Biology Genes Plant computer.software_genre Physcomitrella patens Genome Genetics Arabidopsis thaliana Regulatory Elements Transcriptional Promoter Regions Genetic Gene Internet Database Microarray analysis techniques food and beverages Oryza Promoter biology.organism_classification Bryopsida VII. Plant databases Transcription Initiation Site Databases Nucleic Acid computer Genome Plant |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkt1027 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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