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Developmental Genomic (AtGenExpress + PPDB promoter motif) Full

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 This collection of Gene Expression Properties are associated with flowering tissues.
AtGenExpress_PPDB_Fruit_Seeds
This collection of Gene Expression Properties are associated with fruit and seed tissues.
AtGenExpress_PPDB_Leaf
This collection of Gene Expression Properties are associated with leaf tissues.
AtGenExpress_PPDB_Root
This collection of Gene Expression Properties are associated with root tissues.
AtGenExpress_PPDB_Seedling
This collection of Gene Expression Properties are associated with seedling tissues.
AtGenExpress_PPDB_Stem
This collection of Gene Expression Properties are associated with stem tissues.
AtGenExpress_PPDB_Whole_Plant
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.
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#LINK
#lang en
#attribution_name GenoCon
#attribution_url http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/all_tag_list.cgi?organism=At
#license http://creativecommons.org/publicdomain/zero/1.0/deed.ja
#file_name Octamer_elements
#download_from http://linkdata.org/work/rdf1s329i
#namespace REGoctamer http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/tag_list.cgi?organism=At&tag=
#property # of entry motif sequence PPDB motif PLACE motif Appropriate position
#object_type_xsd integer string:en string:en string:en float
#property_context Assertion Assertion Assertion Assertion Assertion
REGoctamer:AtREG351 328 GGGCCTTA | TAAGGCCC GCCCA GGGCC 119.5
REGoctamer:AtREG352 678 ATTGGGCC | GGCCCAAT GCCCA GGGCC, TGGGCY 119.5
REGoctamer:AtREG353 782 AAGGCCCA | TGGGCCTT GCCCA GGGCC, TGGGCY 116.5
REGoctamer:AtREG354 843 AGGCCCAT | ATGGGCCT GCCCA GGGCC, TGGGCY 112.5
REGoctamer:AtREG355 664 GCCCAATA | TATTGGGC GCCCA 117.5
REGoctamer:AtREG356 724 AGGCCCAA | TTGGGCCT GCCCA GGGCC, TGGGCY 119.5
REGoctamer:AtREG357 755 GCCCATTA | TAATGGGC GCCCA 114.5
REGoctamer:AtREG358 599 TAGGCCCA | TGGGCCTA GCCCA GGGCC, TGGGCY 114.5
REGoctamer:AtREG359 368 AAAGGCCC | GGGCCTTT GCCCA GGGCC 109.5
REGoctamer:AtREG360 305 GGGCCTAA | TTAGGCCC GCCCA GGGCC 116.5
REGoctamer:AtREG361 795 AATGGGCC | GGCCCATT GCCCA GGGCC, TGGGCY 114.5
REGoctamer:AtREG362 235 ATAGGCCC | GGGCCTAT GCCCA GGGCC 114
REGoctamer:AtREG363 34 CTGGGCCC | GGGCCCAG GCCCA GGGCC, TGGGCY 124.5
REGoctamer:AtREG364 407 GGCCCATA | TATGGGCC GCCCA GGGCC, TGGGCY 108.5
REGoctamer:AtREG365 363 GGGCTTTA | TAAAGCCC GCCCA 116.5
REGoctamer:AtREG366 484 CACGTGTC | GACACGTG ACGT ACGT, ACGTG, CACGTG, ACGTGKC, ACACNNG, ACGTGTC 114.5
REGoctamer:AtREG367 372 CACGTGGC | GCCACGTG ACGT ACGT, ACGTG, GCCAC, CACGTG, ACGTGKC, CACGTGGC 115.5
REGoctamer:AtREG368 166 ACGGCCCA | TGGGCCGT GCCCA GGGCC, TGGGCY 107.5
REGoctamer:AtREG369 52 ACGCTGCG | CGCAGCGT 120.5
REGoctamer:AtREG370 234 CAGGCCCA | TGGGCCTG GCCCA GGGCC, TGGGCY 120.5
REGoctamer:AtREG371 187 ACGTGGCG | CGCCACGT ACGT ACGT, ACGTG, GCCAC, ACGTGKC 117
REGoctamer:AtREG372 605 AATGGGCT | AGCCCATT GCCCA TGGGCY 120.5
REGoctamer:AtREG373 467 GGCCCAAA | TTTGGGCC GCCCA GGGCC, TGGGCY 122.5
REGoctamer:AtREG374 110 GGGCCTGA | TCAGGCCC GCCCA GGGCC 114.5
REGoctamer:AtREG375 167 CCGACCCG | CGGGTCGG CCGAC CCGAC 97.5
REGoctamer:AtREG376 877 AAAGCCCA | TGGGCTTT GCCCA TGGGCY 117.5
REGoctamer:AtREG377 77 AACGGCCC | GGGCCGTT GCCCA, AAACG(C/G) GGGCC 112
REGoctamer:AtREG378 747 AAGCCCAT | ATGGGCTT GCCCA TGGGCY 116.5
REGoctamer:AtREG379 350 ACGTGGCA | TGCCACGT ACGT ACGT, ACGTG, GCCAC, ACGTGKC 114.5
REGoctamer:AtREG380 228 ATGGGCCG | CGGCCCAT GCCCA GGGCC, TGGGCY 107.5
REGoctamer:AtREG381 124 AGCGCGTG | CACGCGCT ACGCGC 136.5
REGoctamer:AtREG382 379 ACACGTGG | CCACGTGT ACGT ACGT, ACGTG, CACGTG, ACACNNG 116.5
REGoctamer:AtREG383 119 CGACCCGA | TCGGGTCG 111.5
REGoctamer:AtREG384 109 ACTGGGCC | GGCCCAGT GCCCA GGGCC, TGGGCY 116
REGoctamer:AtREG385 71 ACACGCGC | GCGCGTGT ACGCGC ACACNNG 127.5
REGoctamer:AtREG386 518 AAATGGGC | GCCCATTT GCCCA 125.5
REGoctamer:AtREG387 40 GGGCCCTA | TAGGGCCC GCCCA GGGCC 149.5
REGoctamer:AtREG388 207 GACGTGGC | GCCACGTC ACGT ACGT, ACGTG, GCCAC, ACGTGKC 111
REGoctamer:AtREG389 360 ACGTGTCA | TGACACGT ACGT ACGT, ACGTG, ACGTGKC, ACGTGTC 121.5
REGoctamer:AtREG390 96 GACCCGAC | GTCGGGTC CCGAC, GGGACCC CCGAC 100.5
REGoctamer:AtREG391 157 ATGGGCCC | GGGCCCAT GCCCA GGGCC, TGGGCY 127
REGoctamer:AtREG392 186 GGGCCCAA | TTGGGCCC GCCCA GGGCC, TGGGCY 129.5
REGoctamer:AtREG393 224 TCGGCCCA | TGGGCCGA GCCCA GGGCC, TGGGCY 116.5
REGoctamer:AtREG394 284 GCCCATAA | TTATGGGC GCCCA 119.5
REGoctamer:AtREG395 112 GCGCGTGA | TCACGCGC ACGCGC 119.5
REGoctamer:AtREG396 495 CCCATTAA | TTAATGGG GCCCA TTAATGG 120.5
REGoctamer:AtREG397 72 GGCCCAGA | TCTGGGCC GCCCA GGGCC, TGGGCY 114.5
REGoctamer:AtREG398 104 CAAGGCCC | GGGCCTTG GCCCA GGGCC 128.5
REGoctamer:AtREG399 61 GCCCGTTA | TAACGGGC ACGGGC YAACKG, CNGTTR 117.5
REGoctamer:AtREG400 84 AGGGCCCA | TGGGCCCT GCCCA GGGCC, TGGGCY 140.5
REGoctamer:AtREG401 72 AACGGGCC | GGCCCGTT AAACG(C/G), ACGGGC, CCAACGG GGGCC 118.5
REGoctamer:AtREG402 459 AGCCCAAT | ATTGGGCT GCCCA TGGGCY 116.5
REGoctamer:AtREG403 150 GATGGGCC | GGCCCATC GCCCA GGGCC, TGGGCY 139.5
REGoctamer:AtREG404 53 CCCGGCCC | GGGCCGGG GCCCA GGGCC 114
REGoctamer:AtREG405 145 ACCCGACC | GGTCGGGT CCGAC CCGAC 92.5
REGoctamer:AtREG406 87 GGTCCCAC | GTGGGACC GGGACCC 134
REGoctamer:AtREG407 719 AAGCCCAA | TTGGGCTT GCCCA TGGGCY 116.5
REGoctamer:AtREG408 269 CACGTGGA | TCCACGTG ACGT ACGT, ACGTG, CACGTG 125.5
REGoctamer:AtREG409 445 AAAAGCCC | GGGCTTTT GCCCA 113.5
REGoctamer:AtREG410 110 AGGCCCAG | CTGGGCCT GCCCA GGGCC, TGGGCY 115.5
REGoctamer:AtREG411 75 AGAGGCCC | GGGCCTCT GCCCA GGGCC 118
REGoctamer:AtREG412 470 CCGGTTTA | TAAACCGG AACCG(G/A) 116.5
REGoctamer:AtREG413 138 GCCACGTA | TACGTGGC ACGT ACGT, ACGTG, GCCAC, ACGTGKC 127.5
REGoctamer:AtREG414 202 CGGCCCAA | TTGGGCCG GCCCA GGGCC, TGGGCY 113.5
REGoctamer:AtREG415 323 AAACGACG | CGTCGTTT 104
REGoctamer:AtREG416 185 GGCCTTAA | TTAAGGCC 120
REGoctamer:AtREG417 451 CCCAATAA | TTATTGGG GCCCA 123
REGoctamer:AtREG418 317 AATTGGGC | GCCCAATT GCCCA 126
REGoctamer:AtREG419 289 CCACGTCA | TGACGTGG ACGT ACGT, ACGTG, TGACGTGG, CCACGTCA 123.5
REGoctamer:AtREG420 279 TGGCCCAA | TTGGGCCA GCCCA GGGCC, TGGGCY 130
REGoctamer:AtREG421 345 ATTTGGGC | GCCCAAAT GCCCA 123
REGoctamer:AtREG422 136 TGGGCCCA | TGGGCCCA GCCCA GGGCC, TGGGCY 129.5
REGoctamer:AtREG423 150 CCGGTTCG | CGAACCGG AACCG(G/A) 123.5
REGoctamer:AtREG424 156 AATAGGCC | GGCCTATT 127.5
REGoctamer:AtREG425 162 ATAAGGCC | GGCCTTAT AACCG(G/A) 120.5
REGoctamer:AtREG426 443 TAAGCCCA | TGGGCTTA GCCCA TGGGCY 118.5
REGoctamer:AtREG427 111 GGGCCGAA | TTCGGCCC GCCCA GGGCC 107
REGoctamer:AtREG428 106 ACGACACG | CGTGTCGT 120.5
REGoctamer:AtREG429 49 ACGGGCCT | AGGCCCGT ACGGGC GGGCC 118.5
REGoctamer:AtREG430 183 GGCCTAAA | TTTAGGCC 119.5
REGoctamer:AtREG431 243 ACGACGTC | GACGTCGT ACGT ACGT 98.5
REGoctamer:AtREG432 332 ATATGGGC | GCCCATAT GCCCA 112.5
REGoctamer:AtREG433 85 ACAGGCCC | GGGCCTGT GCCCA GGGCC 128.5
REGoctamer:AtREG434 77 GCCCAGTA | TACTGGGC GCCCA 116.5
REGoctamer:AtREG435 59 GGGCCTAC | GTAGGCCC GCCCA GGGCC 118
REGoctamer:AtREG436 395 AAACCGGT | ACCGGTTT AACCG(G/A) 119
REGoctamer:AtREG437 215 ATGGCCCA | TGGGCCAT GCCCA GGGCC, TGGGCY 139
REGoctamer:AtREG438 152 ATGACACG | CGTGTCAT 128.5
REGoctamer:AtREG439 79 AACGACGC | GCGTCGTT 104.5
* Row count is limited to 100.