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GenoCon2 Challenge A - Developmental Genomic (AtGenExpress + PPDB promoter motif)

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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 tissues, 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).

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
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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/rdf1s219i
#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 GCCCA GGGCC 119.5
REGoctamer:AtREG352 678 ATTGGGCC GCCCA GGGCC, TGGGCY 119.5
REGoctamer:AtREG353 782 AAGGCCCA GCCCA GGGCC, TGGGCY 116.5
REGoctamer:AtREG354 843 AGGCCCAT GCCCA GGGCC, TGGGCY 112.5
REGoctamer:AtREG355 664 GCCCAATA GCCCA 117.5
REGoctamer:AtREG356 724 AGGCCCAA GCCCA GGGCC, TGGGCY 119.5
REGoctamer:AtREG357 755 GCCCATTA GCCCA 114.5
REGoctamer:AtREG358 599 TAGGCCCA GCCCA GGGCC, TGGGCY 114.5
REGoctamer:AtREG359 368 AAAGGCCC GCCCA GGGCC 109.5
REGoctamer:AtREG360 305 GGGCCTAA GCCCA GGGCC 116.5
REGoctamer:AtREG361 795 AATGGGCC GCCCA GGGCC, TGGGCY 114.5
REGoctamer:AtREG362 235 ATAGGCCC GCCCA GGGCC 114
REGoctamer:AtREG363 34 CTGGGCCC GCCCA GGGCC, TGGGCY 124.5
REGoctamer:AtREG364 407 GGCCCATA GCCCA GGGCC, TGGGCY 108.5
REGoctamer:AtREG365 363 GGGCTTTA GCCCA 116.5
REGoctamer:AtREG366 484 CACGTGTC ACGT ACGT, ACGTG, CACGTG, ACGTGKC, ACACNNG, ACGTGTC 114.5
REGoctamer:AtREG367 372 CACGTGGC ACGT ACGT, ACGTG, GCCAC, CACGTG, ACGTGKC, CACGTGGC 115.5
REGoctamer:AtREG368 166 ACGGCCCA GCCCA GGGCC, TGGGCY 107.5
REGoctamer:AtREG369 52 ACGCTGCG 120.5
REGoctamer:AtREG370 234 CAGGCCCA GCCCA GGGCC, TGGGCY 120.5
REGoctamer:AtREG371 187 ACGTGGCG ACGT ACGT, ACGTG, GCCAC, ACGTGKC 117
REGoctamer:AtREG372 605 AATGGGCT GCCCA TGGGCY 120.5
REGoctamer:AtREG373 467 GGCCCAAA GCCCA GGGCC, TGGGCY 122.5
REGoctamer:AtREG374 110 GGGCCTGA GCCCA GGGCC 114.5
REGoctamer:AtREG375 167 CCGACCCG CCGAC CCGAC 97.5
REGoctamer:AtREG376 877 AAAGCCCA GCCCA TGGGCY 117.5
REGoctamer:AtREG377 77 AACGGCCC GCCCA, AAACG(C/G) GGGCC 112
REGoctamer:AtREG378 747 AAGCCCAT GCCCA TGGGCY 116.5
REGoctamer:AtREG379 350 ACGTGGCA ACGT ACGT, ACGTG, GCCAC, ACGTGKC 114.5
REGoctamer:AtREG380 228 ATGGGCCG GCCCA GGGCC, TGGGCY 107.5
REGoctamer:AtREG381 124 AGCGCGTG ACGCGC 136.5
REGoctamer:AtREG382 379 ACACGTGG ACGT ACGT, ACGTG, CACGTG, ACACNNG 116.5
REGoctamer:AtREG383 119 CGACCCGA 111.5
REGoctamer:AtREG384 109 ACTGGGCC GCCCA GGGCC, TGGGCY 116
REGoctamer:AtREG385 71 ACACGCGC ACGCGC ACACNNG 127.5
REGoctamer:AtREG386 518 AAATGGGC GCCCA 125.5
REGoctamer:AtREG387 40 GGGCCCTA GCCCA GGGCC 149.5
REGoctamer:AtREG388 207 GACGTGGC ACGT ACGT, ACGTG, GCCAC, ACGTGKC 111
REGoctamer:AtREG389 360 ACGTGTCA ACGT ACGT, ACGTG, ACGTGKC, ACGTGTC 121.5
REGoctamer:AtREG390 96 GACCCGAC CCGAC, GGGACCC CCGAC 100.5
REGoctamer:AtREG391 157 ATGGGCCC GCCCA GGGCC, TGGGCY 127
REGoctamer:AtREG392 186 GGGCCCAA GCCCA GGGCC, TGGGCY 129.5
REGoctamer:AtREG393 224 TCGGCCCA GCCCA GGGCC, TGGGCY 116.5
REGoctamer:AtREG394 284 GCCCATAA GCCCA 119.5
REGoctamer:AtREG395 112 GCGCGTGA ACGCGC 119.5
REGoctamer:AtREG396 495 CCCATTAA GCCCA TTAATGG 120.5
REGoctamer:AtREG397 72 GGCCCAGA GCCCA GGGCC, TGGGCY 114.5
REGoctamer:AtREG398 104 CAAGGCCC GCCCA GGGCC 128.5
REGoctamer:AtREG399 61 GCCCGTTA ACGGGC YAACKG, CNGTTR 117.5
REGoctamer:AtREG400 84 AGGGCCCA GCCCA GGGCC, TGGGCY 140.5
REGoctamer:AtREG401 72 AACGGGCC AAACG(C/G), ACGGGC, CCAACGG GGGCC 118.5
REGoctamer:AtREG402 459 AGCCCAAT GCCCA TGGGCY 116.5
REGoctamer:AtREG403 150 GATGGGCC GCCCA GGGCC, TGGGCY 139.5
REGoctamer:AtREG404 53 CCCGGCCC GCCCA GGGCC 114
REGoctamer:AtREG405 145 ACCCGACC CCGAC CCGAC 92.5
REGoctamer:AtREG406 87 GGTCCCAC GGGACCC 134
REGoctamer:AtREG407 719 AAGCCCAA GCCCA TGGGCY 116.5
REGoctamer:AtREG408 269 CACGTGGA ACGT ACGT, ACGTG, CACGTG 125.5
REGoctamer:AtREG409 445 AAAAGCCC GCCCA 113.5
REGoctamer:AtREG410 110 AGGCCCAG GCCCA GGGCC, TGGGCY 115.5
REGoctamer:AtREG411 75 AGAGGCCC GCCCA GGGCC 118
REGoctamer:AtREG412 470 CCGGTTTA AACCG(G/A) 116.5
REGoctamer:AtREG413 138 GCCACGTA ACGT ACGT, ACGTG, GCCAC, ACGTGKC 127.5
REGoctamer:AtREG414 202 CGGCCCAA GCCCA GGGCC, TGGGCY 113.5
REGoctamer:AtREG415 323 AAACGACG 104
REGoctamer:AtREG416 185 GGCCTTAA 120
REGoctamer:AtREG417 451 CCCAATAA GCCCA 123
REGoctamer:AtREG418 317 AATTGGGC GCCCA 126
REGoctamer:AtREG419 289 CCACGTCA ACGT ACGT, ACGTG, TGACGTGG, CCACGTCA 123.5
REGoctamer:AtREG420 279 TGGCCCAA GCCCA GGGCC, TGGGCY 130
REGoctamer:AtREG421 345 ATTTGGGC GCCCA 123
REGoctamer:AtREG422 136 TGGGCCCA GCCCA GGGCC, TGGGCY 129.5
REGoctamer:AtREG423 150 CCGGTTCG AACCG(G/A) 123.5
REGoctamer:AtREG424 156 AATAGGCC 127.5
REGoctamer:AtREG425 162 ATAAGGCC AACCG(G/A) 120.5
REGoctamer:AtREG426 443 TAAGCCCA GCCCA TGGGCY 118.5
REGoctamer:AtREG427 111 GGGCCGAA GCCCA GGGCC 107
REGoctamer:AtREG428 106 ACGACACG 120.5
REGoctamer:AtREG429 49 ACGGGCCT ACGGGC GGGCC 118.5
REGoctamer:AtREG430 183 GGCCTAAA 119.5
REGoctamer:AtREG431 243 ACGACGTC ACGT ACGT 98.5
REGoctamer:AtREG432 332 ATATGGGC GCCCA 112.5
REGoctamer:AtREG433 85 ACAGGCCC GCCCA GGGCC 128.5
REGoctamer:AtREG434 77 GCCCAGTA GCCCA 116.5
REGoctamer:AtREG435 59 GGGCCTAC GCCCA GGGCC 118
REGoctamer:AtREG436 395 AAACCGGT AACCG(G/A) 119
REGoctamer:AtREG437 215 ATGGCCCA GCCCA GGGCC, TGGGCY 139
REGoctamer:AtREG438 152 ATGACACG 128.5
REGoctamer:AtREG439 79 AACGACGC 104.5
* Row count is limited to 100.