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PPDB (Plant Promoter DataBase)

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The Plant Promoter Database (PPDB) uses word frequency analysis to identify 8 base-pair motifs in promoters. Motifs are categorized as TATA-box, Y-patch (a CT-rich region often found in plant TATA box promoters), the initiator near the transcription start site, and cis-regulatory motifs. The regulatory motifs are a group of 308 8 base-pair sequences which are used to represent regulatory sites.

References (for PPDB):
http://www.ncbi.nlm.nih.gov/pubmed/17947329
http://www.ncbi.nlm.nih.gov/pubmed/17346352

Descriptions for each data table:
PPDB_MPSS The Plant Promoter Database (PPDB) also deposits the data of transcription start sites (TSSs) detected by the CT-MPSS method. The CT-MPSS method is a combination of cap trapper (CT), a reliable method for preparing the 5' end of full-length cDNA, and massively parallel signature sequencing (MPSS), which enables ultra-parallel sequencing in a considerably shorter time and at lower cost than conventional sequencing methods.
PPDB_reliable_LDSS The Plant Promoter Database (PPDB) uses word frequency analysis to identify 8 base-pair motifs in promoters. Motifs are categorized as TATA-box, Y-patch (a CT-rich region often found in plant TATA box promoters), the initiator near the transcription start site, and cis-regulatory motifs. The regulatory motifs are a group of 308 8 base-pair sequences which are used to represent regulatory sites.


License

We would like to thank Dr. Yoshiharu Yamamoto for supplying the data of PPDB (Plant Promoter Database) for PromoterCAD & GenoCon2 competition. License of this work's data is according to the intentions of the PPDB original data source.
http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi

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File Name
PPDB_MPSS
Table Data (Text)
2013.5.10
2.0MB
クリエイティブ・コモンズ・ライセンス
Table Data (Excel)
2013.5.10
6.2MB
クリエイティブ・コモンズ・ライセンス
RDF (Turtle)
2013.5.10
4.6MB
クリエイティブ・コモンズ・ライセンス
PPDB_reliable_LDSS
Table Data (Text)
2013.5.10
15.1MB
クリエイティブ・コモンズ・ライセンス
Table Data (Excel)
2013.5.10
14.2MB
クリエイティブ・コモンズ・ライセンス
RDF (Turtle)
2013.5.10
27.3MB
クリエイティブ・コモンズ・ライセンス
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Total downloads 208
Created date Dec 27, 2012
Last update date May 10, 2013

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