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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 Koro NISHIKATA
#attribution_url http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/
#license http://creativecommons.org/publicdomain/zero/1.0/deed.ja
#file_name AtGenExpress_PPDB_Whole_Plant
#download_from http://linkdata.org/work/rdf1s219i
#namespace Flowering http://linkdata.org/work/rdf1s220i/Flowering.html#
#namespace Fruit_Seeds http://linkdata.org/work/rdf1s220i/Fruit_Seeds.html#
#namespace Gene http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/display.cgi?organism=At&gene=
#namespace Leaf http://linkdata.org/work/rdf1s220i/Leaf.html#
#namespace OctamerElement http://linkdata.org/work/rdf1s219i/Octamer_elements.html#
#namespace Root http://linkdata.org/work/rdf1s220i/Root.html#
#namespace Seedling http://linkdata.org/work/rdf1s220i/Seedling.html#
#namespace Stem http://linkdata.org/work/rdf1s220i/Stem.html#
#namespace TAIR http://arabidopsis.org/servlets/TairObject?type=locus&name=
#namespace Whole_Plant http://linkdata.org/work/rdf1s220i/Whole_Plant.html#
#namespace genome_version http://www.arabidopsis.org/portals/genAnnotation/gene_structural_annotation/
#property PPDB motif motif type motif sequence motif position genome_version:annotation_data.jsp TAIR gene chromosome position start position start from TSS peak position end position end from TSS peak strand sequence TSS peak position TSS peak position from Initiation codon Whole_Plant:ATGE_22 Whole_Plant:ATGE_23 Whole_Plant:ATGE_24
#object_type_xsd string:en string:en string:en float string:en string:en string:en integer integer integer integer string:en string:en integer integer float float float
#property_context Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion
Gene:AT1G01010 OctamerElement:AtREG514 | OctamerElement:AtREG519 REG TCGGTTTA | CGGTTTAC 209.5 | 208.5 TAIR9 TAIR:At1g01010 Chr1 3455 | 3456 -213 | -212 3462 | 3463 -206 | -205 + 3668 -92 3760 -0.4018 -0.1280 -0.0707
Gene:AT1G01010 OctamerElement:AtREG473 | OctamerElement:AtREG412 | OctamerElement:AtREG521 REG TTAAACCG | TAAACCGG | AAACCGGA 129.5 | 128.5 | 127.5 TAIR9 TAIR:At1g01010 Chr1 3535 | 3536 | 3537 -133 | -132 | -131 3542 | 3543 | 3544 -126 | -125 | -124 + 3668 -92 3760 -0.4018 -0.1280 -0.0707
Gene:AT1G01010 OctamerElement:AtREG626 REG AAACGCTG 63.5 TAIR9 TAIR:At1g01010 Chr1 3601 -67 3608 -60 + 3668 -92 3760 -0.4018 -0.1280 -0.0707
Gene:AT1G01060 OctamerElement:AtREG623 REG ATACCCTT 130.5 TAIR9 TAIR:At1g01060 Chr1 37913 134 37906 127 - 37779 718 37061 -0.1273 0.6275 0.6216
Gene:AT1G01060 OctamerElement:AtREG478 | OctamerElement:AtREG366 | OctamerElement:AtREG382 | OctamerElement:AtREG544 REG ACGTGTCG | CACGTGTC | CCACGTGT | ACCACGTG 167.5 | 168.5 | 169.5 | 170.5 TAIR9 TAIR:At1g01060 Chr1 37950 | 37951 | 37952 | 37953 171 | 172 | 173 | 174 37943 | 37944 | 37945 | 37946 164 | 165 | 166 | 167 - 37779 718 37061 -0.1273 0.6275 0.6216
Gene:AT1G01070 OctamerElement:AtREG462 REG GGGCTTAT 68.5 TAIR9 TAIR:At1g01070 Chr1 40933 72 40926 65 - 40861 264 40597 0.2694 0.4306 0.1483
Gene:AT1G01080 OctamerElement:AtREG375 | OctamerElement:AtREG442 | OctamerElement:AtREG405 | OctamerElement:AtREG390 | OctamerElement:AtREG617 REG CCGACCCG | CCCGACCC | ACCCGACC | GACCCGAC | TGACCCGA 43.5 | 44.5 | 45.5 | 46.5 | 47.5 TAIR9 TAIR:At1g01080 Chr1 46877 | 46878 | 46879 | 46880 | 46881 47 | 48 | 49 | 50 | 51 46870 | 46871 | 46872 | 46873 | 46874 40 | 41 | 42 | 43 | 44 - 46830 41 46789 1.1337 1.2453 0.9973
Gene:AT1G01080 OctamerElement:AtREG459 | OctamerElement:AtREG359 | OctamerElement:AtREG353 | OctamerElement:AtREG356 | OctamerElement:AtREG373 REG GGCCTTTT | GGGCCTTT | TGGGCCTT | TTGGGCCT | TTTGGGCC 144.5 | 145.5 | 146.5 | 147.5 | 148.5 TAIR9 TAIR:At1g01080 Chr1 46978 | 46979 | 46980 | 46981 | 46982 148 | 149 | 150 | 151 | 152 46971 | 46972 | 46973 | 46974 | 46975 141 | 142 | 143 | 144 | 145 - 46830 41 46789 1.1337 1.2453 0.9973
Gene:AT1G01080 OctamerElement:AtREG437 | OctamerElement:AtREG490 | OctamerElement:AtREG361 | OctamerElement:AtREG643 REG TGGGCCAT | ATGGGCCA | AATGGGCC | GAATGGGC 285.5 | 286.5 | 287.5 | 288.5 TAIR9 TAIR:At1g01080 Chr1 47119 | 47120 | 47121 | 47122 289 | 290 | 291 | 292 47112 | 47113 | 47114 | 47115 282 | 283 | 284 | 285 - 46830 41 46789 1.1337 1.2453 0.9973
Gene:AT1G01090 OctamerElement:AtREG523 REG GTGGGTCC 90.5 TAIR9 TAIR:At1g01090 Chr1 49365 94 49358 87 - 49271 105 49166 -0.1694 -0.1300 -0.1552
Gene:AT2G26530 OctamerElement:AtREG473 | OctamerElement:AtREG652 REG CGGTTTAA | ACGGTTTA 77.5 | 78.5 TAIR9 TAIR:At2g26530 Chr2 11284099 | 11284100 81 | 82 11284092 | 11284093 74 | 75 - 11284018 29 11283989 1.7532 -0.3318 -0.0133
Gene:AT2G26530 OctamerElement:AtREG571 | OctamerElement:AtREG581 | OctamerElement:AtREG372 | OctamerElement:AtREG386 REG TGGGCTAA | ATGGGCTA | AATGGGCT | AAATGGGC 251.5 | 252.5 | 253.5 | 254.5 TAIR9 TAIR:At2g26530 Chr2 11284273 | 11284274 | 11284275 | 11284276 255 | 256 | 257 | 258 11284266 | 11284267 | 11284268 | 11284269 248 | 249 | 250 | 251 - 11284018 29 11283989 1.7532 -0.3318 -0.0133
Gene:AT2G26570 OctamerElement:AtREG494 | OctamerElement:AtREG375 | OctamerElement:AtREG442 | OctamerElement:AtREG405 REG CCGGGTCG | CGGGTCGG | GGGTCGGG | GGTCGGGT 273.5 | 272.5 | 271.5 | 270.5 TAIR9 TAIR:At2g26570 Chr2 11298756 | 11298757 | 11298758 | 11298759 -277 | -276 | -275 | -274 11298763 | 11298764 | 11298765 | 11298766 -270 | -269 | -268 | -267 + 11299033 -532 11299565 0.3323 0.2215 0.3601
Gene:AT2G26570 OctamerElement:AtREG513 REG ACGTGGAC 134.5 TAIR9 TAIR:At2g26570 Chr2 11298895 -138 11298902 -131 + 11299033 -532 11299565 0.3323 0.2215 0.3601
Gene:AT2G26590 OctamerElement:AtREG525 | OctamerElement:AtREG407 | OctamerElement:AtREG402 REG TGGGCTTG | TTGGGCTT | ATTGGGCT 107.5 | 108.5 | 109.5 TAIR9 TAIR:At2g26590 Chr2 11315188 | 11315189 | 11315190 111 | 112 | 113 11315181 | 11315182 | 11315183 104 | 105 | 106 - 11315077 360 11314717 -0.3075 -0.0958 -0.2317
Gene:AT2G26590 OctamerElement:AtREG549 REG TAAAAGCC 135.5 TAIR9 TAIR:At2g26590 Chr2 11315216 139 11315209 132 - 11315077 360 11314717 -0.3075 -0.0958 -0.2317
Gene:AT2G26590 OctamerElement:AtREG578 | OctamerElement:AtREG483 | OctamerElement:AtREG606 REG ACGTCATC | CACGTCAT | TGTCACGT 271.5 | 272.5 | 275.5 TAIR9 TAIR:At2g26590 Chr2 11315352 | 11315353 | 11315356 275 | 276 | 279 11315345 | 11315346 | 11315349 268 | 269 | 272 - 11315077 360 11314717 -0.3075 -0.0958 -0.2317
Gene:AT1G01050 At180 | At207 | At261 | At290 TATA TATATACA | ATATATAC | CATATATA | TCATATAT 26.5 | 27.5 | 28.5 | 29.5 TAIR9 TAIR:At1g01050 Chr1 33147 | 33148 | 33149 | 33150 30 | 31 | 32 | 33 33140 | 33141 | 33142 | 33143 23 | 24 | 25 | 26 - 33117 447 32670 0.1613 0.1834 0.0315
Gene:AT1G01070 At153 TATA ATATAGAG 26.5 TAIR9 TAIR:At1g01070 Chr1 40891 30 40884 23 - 40861 264 40597 0.2694 0.4306 0.1483
Gene:AT2G26560 At227 | At231 | At281 | At304 TATA TATAAATA | CTATAAAT | CCTATAAA | TCCTATAA 27.5 | 28.5 | 29.5 | 30.5 TAIR9 TAIR:At2g26560 Chr2 11295837 | 11295838 | 11295839 | 11295840 31 | 32 | 33 | 34 11295830 | 11295831 | 11295832 | 11295833 24 | 25 | 26 | 27 - 11295806 98 11295708 3.1533 1.6392 2.5577
Gene:AT1G01010 At708 | At121 | At050 Y CTTCCTCC | CCTCCCTC | CTCCCTCC 45.5 | 42.5 | 41.5 TAIR9 TAIR:At1g01010 Chr1 3619 | 3622 | 3623 -49 | -46 | -45 3626 | 3629 | 3630 -42 | -39 | -38 + 3668 -92 3760 -0.4018 -0.1280 -0.0707
Gene:AT1G01050 At033 | At026 | At006 Y TCTCTCCC | TTCTCTCC | TTTCTCTC 20.5 | 19.5 | 18.5 TAIR9 TAIR:At1g01050 Chr1 33100 | 33101 | 33102 -17 | -16 | -15 33093 | 33094 | 33095 -24 | -23 | -22 - 33117 447 32670 0.1613 0.1834 0.0315
Gene:AT1G01060 At063 | At073 | At051 | At063 | At073 | At051 | At063 | At073 | At051 | At063 | At073 | At051 | At063 | At073 | At051 | At063 | At073 | At051 | At063 | At073 | At051 | At063 | At073 | At051 | At063 | At073 | At051 | At063 | At073 | At051 | At066 | At713 | At085 | At088 | At715 Y TCTTCTTC | TTCTTCTT | CTTCTTCT | TCTTCTTC | TTCTTCTT | CTTCTTCT | TCTTCTTC | TTCTTCTT | CTTCTTCT | TCTTCTTC | TTCTTCTT | CTTCTTCT | TCTTCTTC | TTCTTCTT | CTTCTTCT | TCTTCTTC | TTCTTCTT | CTTCTTCT | TCTTCTTC | TTCTTCTT | CTTCTTCT | TCTTCTTC | TTCTTCTT | CTTCTTCT | TCTTCTTC | TTCTTCTT | CTTCTTCT | TCTTCTTC | TTCTTCTT | CTTCTTCT | CCTTCTTC | TCCTTCTT | TTCCTTCT | CTTCCTTC | TCTTCCTT 39.5 | 38.5 | 37.5 | 36.5 | 35.5 | 34.5 | 33.5 | 32.5 | 31.5 | 30.5 | 29.5 | 28.5 | 27.5 | 26.5 | 25.5 | 24.5 | 23.5 | 22.5 | 21.5 | 20.5 | 19.5 | 18.5 | 17.5 | 16.5 | 15.5 | 14.5 | 13.5 | 12.5 | 11.5 | 10.5 | 9.5 | 8.5 | 7.5 | 6.5 | 5.5 TAIR9 TAIR:At1g01060 Chr1 37743 | 37744 | 37745 | 37746 | 37747 | 37748 | 37749 | 37750 | 37751 | 37752 | 37753 | 37754 | 37755 | 37756 | 37757 | 37758 | 37759 | 37760 | 37761 | 37762 | 37763 | 37764 | 37765 | 37766 | 37767 | 37768 | 37769 | 37770 | 37771 | 37772 | 37773 | 37774 | 37775 | 37776 | 37777 -36 | -35 | -34 | -33 | -32 | -31 | -30 | -29 | -28 | -27 | -26 | -25 | -24 | -23 | -22 | -21 | -20 | -19 | -18 | -17 | -16 | -15 | -14 | -13 | -12 | -11 | -10 | -9 | -8 | -7 | -6 | -5 | -4 | -3 | -2 37736 | 37737 | 37738 | 37739 | 37740 | 37741 | 37742 | 37743 | 37744 | 37745 | 37746 | 37747 | 37748 | 37749 | 37750 | 37751 | 37752 | 37753 | 37754 | 37755 | 37756 | 37757 | 37758 | 37759 | 37760 | 37761 | 37762 | 37763 | 37764 | 37765 | 37766 | 37767 | 37768 | 37769 | 37770 -43 | -42 | -41 | -40 | -39 | -38 | -37 | -36 | -35 | -34 | -33 | -32 | -31 | -30 | -29 | -28 | -27 | -26 | -25 | -24 | -23 | -22 | -21 | -20 | -19 | -18 | -17 | -16 | -15 | -14 | -13 | -12 | -11 | -10 | -9 - 37779 718 37061 -0.1273 0.6275 0.6216
Gene:AT1G01060 At063 Y TCTTCTTC 14.5 TAIR9 TAIR:At1g01060 Chr1 37797 18 37790 11 - 37779 718 37061 -0.1273 0.6275 0.6216
Gene:AT1G01060 At042 | At063 | At073 | At051 | At063 | At073 | At051 | At063 | At075 | At083 | At040 | At009 Y CTTCTTCC | TCTTCTTC | TTCTTCTT | CTTCTTCT | TCTTCTTC | TTCTTCTT | CTTCTTCT | TCTTCTTC | CTCTTCTT | TCTCTTCT | TTCTCTTC | CTTCTCTT 24.5 | 25.5 | 26.5 | 27.5 | 28.5 | 29.5 | 30.5 | 31.5 | 32.5 | 33.5 | 34.5 | 35.5 TAIR9 TAIR:At1g01060 Chr1 37807 | 37808 | 37809 | 37810 | 37811 | 37812 | 37813 | 37814 | 37815 | 37816 | 37817 | 37818 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 37800 | 37801 | 37802 | 37803 | 37804 | 37805 | 37806 | 37807 | 37808 | 37809 | 37810 | 37811 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 - 37779 718 37061 -0.1273 0.6275 0.6216
Gene:AT1G01080 At005 Y TTCTTCTC 8.5 TAIR9 TAIR:At1g01080 Chr1 46825 -5 46818 -12 - 46830 41 46789 1.1337 1.2453 0.9973
Gene:AT1G01090 At090 Y CTCTCTTT 29.5 TAIR9 TAIR:At1g01090 Chr1 49245 -26 49238 -33 - 49271 105 49166 -0.1694 -0.1300 -0.1552
Gene:AT1G01090 At026 Y TTCTCTCC 10.5 TAIR9 TAIR:At1g01090 Chr1 49264 -7 49257 -14 - 49271 105 49166 -0.1694 -0.1300 -0.1552
Gene:AT1G01090 At114 Y CCTCCTCT 12.5 TAIR9 TAIR:At1g01090 Chr1 49287 16 49280 9 - 49271 105 49166 -0.1694 -0.1300 -0.1552
Gene:AT2G26500 At710 | At348 | At712 | At701 Y TCCTCCTT | CCTCCTTC | TCCTTCCT | CCTTCCTT 45.5 | 44.5 | 42.5 | 41.5 TAIR9 TAIR:At2g26500 Chr2 11270177 | 11270178 | 11270180 | 11270181 -49 | -48 | -46 | -45 11270184 | 11270185 | 11270187 | 11270188 -42 | -41 | -39 | -38 + 11270226 -144 11270370 1.2327 1.1989 1.1943
Gene:AT2G26500 At004 | At009 | At040 | At083 | At075 Y TCTTCTCT | CTTCTCTT | TTCTCTTC | TCTCTTCT | CTCTTCTT 25.5 | 24.5 | 23.5 | 22.5 | 21.5 TAIR9 TAIR:At2g26500 Chr2 11270197 | 11270198 | 11270199 | 11270200 | 11270201 -29 | -28 | -27 | -26 | -25 11270204 | 11270205 | 11270206 | 11270207 | 11270208 -22 | -21 | -20 | -19 | -18 + 11270226 -144 11270370 1.2327 1.1989 1.1943
Gene:AT2G26500 At020 | At717 | At060 Y CTTCTCCT | TTCTCCTT | CTCCTTTC 10.5 | 9.5 | 7.5 TAIR9 TAIR:At2g26500 Chr2 11270212 | 11270213 | 11270215 -14 | -13 | -11 11270219 | 11270220 | 11270222 -7 | -6 | -4 + 11270226 -144 11270370 1.2327 1.1989 1.1943
Gene:AT2G26500 At009 Y CTTCTCTT 14.5 TAIR9 TAIR:At2g26500 Chr2 11270237 11 11270244 18 + 11270226 -144 11270370 1.2327 1.1989 1.1943
Gene:AT2G26510 At004 | At009 Y TCTTCTCT | CTTCTCTT 33.5 | 34.5 TAIR9 TAIR:At2g26510 Chr2 11273999 | 11274000 30 | 31 11274006 | 11274007 37 | 38 + 11273969 -149 11274118 -0.1267 -0.0819 -0.0721
Gene:AT2G26530 At005 | At051 | At066 Y TTCTTCTC | CTTCTTCT | CCTTCTTC 19.5 | 20.5 | 21.5 TAIR9 TAIR:At2g26530 Chr2 11284041 | 11284042 | 11284043 23 | 24 | 25 11284034 | 11284035 | 11284036 16 | 17 | 18 - 11284018 29 11283989 1.7532 -0.3318 -0.0133
Gene:AT2G26580 At705 | At079 | At035 Y CTCTCCTT | CCTCTCCT | TCCTCTCC 41.5 | 40.5 | 39.5 TAIR9 TAIR:At2g26580 Chr2 11306971 | 11306972 | 11306973 -38 | -37 | -36 11306964 | 11306965 | 11306966 -45 | -44 | -43 - 11307009 270 11306739 0.7656 0.8863 0.7128
Gene:AT2G26590 At026 | At006 | At008 | At007 Y TTCTCTCC | TTTCTCTC | CTTTCTCT | TCTTTCTC 19.5 | 18.5 | 17.5 | 16.5 TAIR9 TAIR:At2g26590 Chr2 11315061 | 11315062 | 11315063 | 11315064 -16 | -15 | -14 | -13 11315054 | 11315055 | 11315056 | 11315057 -23 | -22 | -21 | -20 - 11315077 360 11314717 -0.3075 -0.0958 -0.2317
Gene:AT1G01010 At723 | At728 | At722 GA CGAGAGAG | GAGAGAGA | AGAGAGAT 32.5 | 33.5 | 34.5 TAIR9 TAIR:At1g01010 Chr1 3697 | 3698 | 3699 29 | 30 | 31 3704 | 3705 | 3706 36 | 37 | 38 + 3668 -92 3760 -0.4018 -0.1280 -0.0707
Gene:AT1G01070 At730 | At722 | At728 | At721 | At731 GA GAGAGATA | AGAGAGAT | GAGAGAGA | AGAGAGAG | TAGAGAGA 19.5 | 20.5 | 21.5 | 22.5 | 23.5 TAIR9 TAIR:At1g01070 Chr1 40884 | 40885 | 40886 | 40887 | 40888 23 | 24 | 25 | 26 | 27 40877 | 40878 | 40879 | 40880 | 40881 16 | 17 | 18 | 19 | 20 - 40861 264 40597 0.2694 0.4306 0.1483
Gene:AT2G26570 At734 | At721 | At728 | At719 GA AAGAGAGA | AGAGAGAG | GAGAGAGA | AGAGAGAA 11.5 | 10.5 | 9.5 | 8.5 TAIR9 TAIR:At2g26570 Chr2 11299018 | 11299019 | 11299020 | 11299021 -15 | -14 | -13 | -12 11299025 | 11299026 | 11299027 | 11299028 -8 | -7 | -6 | -5 + 11299033 -532 11299565 0.3323 0.2215 0.3601
Gene:AT2G26570 At730 GA GAGAGATA 28.5 TAIR9 TAIR:At2g26570 Chr2 11299058 25 11299065 32 + 11299033 -532 11299565 0.3323 0.2215 0.3601
* Row count is limited to 100.