Contact

Link and Publish your data

to the Linked Open Data Community

Linkdata Work Information

PPDB (Plant Promoter DataBase)

Open Smart Phone View

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

0

value

useful
0
Loading...

published applications using data of this Linkdata work.