Developmental Genomic (AtGenExpress + PPDB promoter motif) median

Developmental Microarray Expression Data (AtGenExpress) of plant developmental tissues, combined with LDSS sequence analysis of regulatory (8mer) motif calculations (PPDB). We took the median of triplicate measurements from AtGenExpress, then sorted the developmental series into plant organs (Flower, Leaf, Root, Stem, Fruit & Seeds), with one category for seedlings (8 days old or less) and another for whole plants (older than 8 days). For each motif, we calculated the position relative to the TSS as determined experimentally (PPDB). Gene Loci without expression data or motif data were removed from this database.

References (for PPDB):
http://www.ncbi.nlm.nih.gov/pubmed/17947329
http://www.ncbi.nlm.nih.gov/pubmed/17346352
References (for AtGenExpress)
http://www.ncbi.nlm.nih.gov/pubmed/15806101

Descriptions for each data table:

AtGenExpress_PPDB_Flowering_median	This collection of Gene Expression Properties are associated with flowering tissues.
AtGenExpress_PPDB_Fruit_Seeds_median	This collection of Gene Expression Properties are associated with fruit and seed tissues.
AtGenExpress_PPDB_Leaf_median	This collection of Gene Expression Properties are associated with leaf tissues.
AtGenExpress_PPDB_Root_median	This collection of Gene Expression Properties are associated with root tissues.
AtGenExpress_PPDB_Seedling_median	This collection of Gene Expression Properties are associated with seedling tissues.
AtGenExpress_PPDB_Stem_median	This collection of Gene Expression Properties are associated with stem tissues.
AtGenExpress_PPDB_Whole_Plant_median	This collection of Gene Expression Properties are associated with whole plant body parts.
Octamer_elements	A list of the 8mer sequence motifs from PPDB. This table lists each 8mer along with the appropriate median position from the TSS, calculated from all 8mers.

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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AtGenExpress_PPDB_Flowering_median			Action Show Table Data Contents Show API List Show Map Validate RDF Reuse Table Data
Table Data (Text)	2013.5.10	8.5MB
Table Data (Excel)	2013.5.10	14.5MB
RDF (Turtle)	2013.5.10	38.6MB
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AtGenExpress_PPDB_Fruit_Seeds_median			Action Show Table Data Contents Show API List Show Map Validate RDF Reuse Table Data
Table Data (Text)	2013.5.10	4.5MB
Table Data (Excel)	2013.5.10	6.9MB
RDF (Turtle)	2013.5.10	15.3MB
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AtGenExpress_PPDB_Leaf_median			Action Show Table Data Contents Show API List Show Map Validate RDF Reuse Table Data
Table Data (Text)	2013.5.10	6.0MB
Table Data (Excel)	2013.5.10	9.5MB
RDF (Turtle)	2013.5.10	23.5MB
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AtGenExpress_PPDB_Root_median			Action Show Table Data Contents Show API List Show Map Validate RDF Reuse Table Data
Table Data (Text)	2013.5.10	4.2MB
Table Data (Excel)	2013.5.10	6.2MB
RDF (Turtle)	2013.5.10	13.6MB
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AtGenExpress_PPDB_Seedling_median			Action Show Table Data Contents Show API List Show Map Validate RDF Reuse Table Data
Table Data (Text)	2013.5.10	5.2MB
Table Data (Excel)	2013.5.10	8.2MB
RDF (Turtle)	2013.5.10	19.6MB
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AtGenExpress_PPDB_Stem_median			Action Show Table Data Contents Show API List Show Map Validate RDF Reuse Table Data
Table Data (Text)	2013.5.10	3.7MB
Table Data (Excel)	2013.5.10	5.1MB
RDF (Turtle)	2013.5.10	10.6MB
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AtGenExpress_PPDB_Whole_Plant_median			Action Show Table Data Contents Show API List Show Map Validate RDF Reuse Table Data
Table Data (Text)	2013.5.10	3.7MB
Table Data (Excel)	2013.5.10	5.1MB
RDF (Turtle)	2013.5.10	10.6MB
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Octamer_elements			Action Show Table Data Contents Show API List Show Map Validate RDF Reuse Table Data
Table Data (Text)	2013.3.8	18.8KB
Table Data (Excel)	2013.3.8	53.0KB
RDF (Turtle)	2013.3.8	119.6KB
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Contributor Send Message	Koro_Nishikata
Collaborators	Robert Cox
Website	http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-... http://arabidopsis.org/servlets/TairOb...
Reference	http://www.ncbi.nlm.nih.gov/pubmed/179... http://www.ncbi.nlm.nih.gov/pubmed/173... http://www.ncbi.nlm.nih.gov/pubmed/158...
Total downloads	594
Created date	Mar 5, 2013
Last update date	May 10, 2013

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Developmental Genomic (AtGenExpress + PPDB promoter motif) median

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