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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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#LINK
#lang en
#attribution_name GenoCon
#attribution_url http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/index.cgi
#file_name PPDB_MPSS
#download_from http://linkdata.org/work/rdf1s459i
#property genome version motif type start end score strand phase attributes
#object_type_xsd string string integer integer string string string string
#property_context Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion
1 tair9 TSS peak 3668 3668 13 + . Sequence " AT1G01010.1 "
1 tair9 TSS peak 45117 45117 4 + .
1 tair9 TSS peak 45868 45868 2 + .
1 tair9 TSS peak 52189 52189 4 + . Sequence " AT1G01110.1,AT1G01110.2 "
1 tair9 TSS peak 73127 73127 2 + .
1 tair9 TSS 75559 75559 2 + . Sequence " AT1G01180.1 "
1 tair9 TSS peak 75585 75585 13 + . Sequence " AT1G01180.1 "
1 tair9 TSS 75606 75606 4 + . Sequence " AT1G01180.1 "
1 tair9 TSS 75614 75614 5 + . Sequence " AT1G01180.1 "
1 tair9 TSS peak 82405 82405 2 + .
1 tair9 TSS peak 88898 88898 4 + . Sequence " AT1G01210.1 "
1 tair9 TSS peak 97452 97452 10 + . Sequence " AT1G01230.1 "
1 tair9 TSS peak 100976 100976 4 + .
1 tair9 TSS peak 101082 101082 2 + .
1 tair9 TSS peak 109052 109052 4 + . Sequence " AT1G01260.1,AT1G01260.2 "
1 tair9 TSS peak 117030 117030 13 + . Sequence " AT1G01300.1 "
1 tair9 TSS 117035 117035 4 + . Sequence " AT1G01300.1 "
1 tair9 TSS 117037 117037 10 + . Sequence " AT1G01300.1 "
1 tair9 TSS 117075 117075 4 + .
1 tair9 TSS 117077 117077 4 + .
1 tair9 TSS peak 117858 117858 4 + .
1 tair9 TSS 142093 142093 5 + . Sequence " AT1G01360.1 "
1 tair9 TSS 142095 142095 2 + . Sequence " AT1G01360.1 "
1 tair9 TSS peak 142100 142100 21 + . Sequence " AT1G01360.1 "
1 tair9 TSS peak 143680 143680 4 + . Sequence " AT1G01370.1,AT1G01370.2 "
1 tair9 TSS peak 163491 163491 2 + .
1 tair9 TSS peak 164007 164007 2 + .
1 tair9 TSS peak 176073 176073 5 + . Sequence " AT1G01480.2 "
1 tair9 TSS peak 185108 185108 2 + . Sequence " AT1G01500.1 "
1 tair9 TSS peak 187217 187217 8 + . Sequence " AT1G01510.1 "
1 tair9 TSS 187227 187227 2 + . Sequence " AT1G01510.1 "
1 tair9 TSS peak 197522 197522 4 + .
1 tair9 TSS peak 199655 199655 17 + . Sequence " AT1G01550.1,AT1G01550.2 "
1 tair9 TSS 199657 199657 13 + . Sequence " AT1G01550.1,AT1G01550.2 "
1 tair9 TSS 199663 199663 5 + . Sequence " AT1G01550.1,AT1G01550.2 "
1 tair9 TSS 199700 199700 4 + . Sequence " AT1G01550.1,AT1G01550.2 "
1 tair9 TSS 199723 199723 5 + . Sequence " AT1G01550.1,AT1G01550.2 "
1 tair9 TSS 201075 201075 4 + .
1 tair9 TSS 201092 201092 5 + .
1 tair9 TSS 201093 201093 4 + .
1 tair9 TSS peak 201127 201127 8 + .
1 tair9 TSS 201387 201387 2 + . Sequence " AT1G01560.1,AT1G01560.2 "
1 tair9 TSS peak 201423 201423 5 + . Sequence " AT1G01560.1,AT1G01560.2 "
1 tair9 TSS peak 220236 220236 4 + .
1 tair9 TSS peak 229043 229043 13 + . Sequence " AT1G01630.1 "
1 tair9 TSS 229046 229046 10 + . Sequence " AT1G01630.1 "
1 tair9 TSS 229071 229071 8 + . Sequence " AT1G01630.1 "
1 tair9 TSS 229072 229072 8 + . Sequence " AT1G01630.1 "
1 tair9 TSS 229136 229136 8 + . Sequence " AT1G01630.1 "
1 tair9 TSS peak 229525 229525 4 + .
1 tair9 TSS peak 249327 249327 2 + .
1 tair9 TSS peak 251406 251406 4 + .
1 tair9 TSS peak 261116 261116 2 + .
1 tair9 TSS peak 262880 262880 4 + . Sequence " AT1G01710.1 "
1 tair9 TSS peak 264318 264318 8 + .
1 tair9 TSS peak 268330 268330 21 + . Sequence " AT1G01720.1 "
1 tair9 TSS peak 268937 268937 2 + .
1 tair9 TSS peak 269455 269455 4 + .
1 tair9 TSS 270982 270982 5 + . Sequence " AT1G01730.1 "
1 tair9 TSS peak 270998 270998 8 + . Sequence " AT1G01730.1 "
1 tair9 TSS peak 271191 271191 5 + .
1 tair9 TSS peak 275437 275437 8 + . Sequence " AT1G01750.1 "
1 tair9 TSS peak 280246 280246 5 + .
1 tair9 TSS peak 282558 282558 4 + . Sequence " AT1G01780.1 "
1 tair9 TSS peak 282757 282757 2 + . Sequence " AT1G01780.1 "
1 tair9 TSS peak 283026 283026 2 + .
1 tair9 TSS peak 284494 284494 4 + . Sequence " AT1G01790.1 "
1 tair9 TSS peak 284522 284522 4 + . Sequence " AT1G01790.1 "
1 tair9 TSS peak 285125 285125 4 + .
1 tair9 TSS peak 285280 285280 2 + .
1 tair9 TSS peak 293379 293379 8 + . Sequence " AT1G01800.1,AT1G01800.2 "
1 tair9 TSS 293390 293390 5 + . Sequence " AT1G01800.1,AT1G01800.2 "
1 tair9 TSS 293401 293401 4 + . Sequence " AT1G01800.2 "
1 tair9 TSS peak 294080 294080 10 + .
1 tair9 TSS peak 294530 294530 4 + . Sequence " AT1G01810.1 "
1 tair9 TSS 294614 294614 2 + . Sequence " AT1G01810.1 "
1 tair9 TSS peak 310324 310324 4 + . Sequence " AT1G01900.1 "
1 tair9 TSS peak 338331 338331 2 + . Sequence " AT1G01970.1 "
1 tair9 TSS peak 345908 345908 2 + . Sequence " AT1G02000.1 "
1 tair9 TSS peak 346037 346037 2 + . Sequence " AT1G02000.1 "
1 tair9 TSS peak 373525 373525 2 + . Sequence " AT1G02080.1 "
1 tair9 TSS peak 373574 373574 2 + . Sequence " AT1G02080.1 "
1 tair9 TSS peak 375326 375326 2 + .
1 tair9 TSS peak 376407 376407 8 + .
1 tair9 TSS peak 376666 376666 4 + .
1 tair9 TSS peak 376926 376926 4 + .
1 tair9 TSS peak 377977 377977 8 + .
1 tair9 TSS peak 381170 381170 4 + .
1 tair9 TSS peak 384194 384194 4 + .
1 tair9 TSS peak 389873 389873 4 + . Sequence " AT1G02100.1,AT1G02100.2,AT1G02100.3 "
1 tair9 TSS peak 389883 389883 4 + .
* Row count is limited to 100.