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GenoCon2 Challenge A - Circadian Coexpression (DIURNAL + ATTED-II promoter motif)

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Circadian Data collected over two days (44 hours) at four hour intervals in various growth conditions. We calculated the Phase of each data by non-linear best fit to a sine wave with a 24 hour period, and similarly calculated the Amplitude. Visually checking the 1000 largest amplitude genes showed a good fit in all cases, though a few genes clearly deviated from sinusoidal behavior. All had a major period of 24 hours. For each gene locus, we added the CEG motifs as calculated by ATTED-II.

References (for ATTED-II):
http://www.ncbi.nlm.nih.gov/pubmed/17130150
References (for DIURNAL)
http://www.ncbi.nlm.nih.gov/pubmed/18419293
15

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#LINK
#lang en
#attribution_name GenoCon_2
#attribution_url http://atted.jp/download.shtml
#license http://creativecommons.org/publicdomain/zero/1.0/deed.ja
#file_name DiurnalHours_ATTED_LDHH_ST
#download_from http://linkdata.org/work/rdf1s288i
#namespace ATTED http://atted.jp/data/locus/
#namespace Circadian_Condition http://linkdata.org/work/rdf1s290i/Circadian_condition.html#
#namespace Diurnal_Condition http://linkdata.org/work/rdf1s290i/Diurnal_condition.html#
#namespace Flowering http://linkdata.org/work/rdf1s220i/Flowering.html#
#namespace Fruit_Seeds http://linkdata.org/work/rdf1s220i/Fruit_Seeds.html#
#namespace HeptamerElement http://linkdata.org/work/rdf1s218i/Heptamer_elements.html#
#namespace Leaf http://linkdata.org/work/rdf1s220i/Leaf.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 Whole_Plant http://linkdata.org/work/rdf1s220i/Whole_Plant.html#
#property motif position motif motif sequence CEG Probe Condition Phase Correlation Expression 0 hours Expression 4 hours Expression 8 hours Expression 12 hours Expression 16 hours Expression 20 hours Expression 24 hours Expression 28 hours Expression 32 hours Expression 36 hours Expression 40 hours Expression 44 hours Sine Phase Sine Amplitude
#object_type_xsd float string string float string string int float float float float float float float float float float float float float float float
#property_context Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion
ATTED:At1g01030.html 49 | 51 | 53 | 88 HeptamerElement:TCTCTCT | HeptamerElement:TCTCTCT | HeptamerElement:TCTCTCT | HeptamerElement:ATGGGCC TCTCTCT | TCTCTCT | TCTCTCT | ATGGGCC 0.06 | 0.07 | 0.06 | 0.08 261568_at Diurnal_Condition:LDHH_ST 20 0.419450 6.960770 7.712810 6.781940 6.972670 6.729500 8.363510 6.876110 7.362270 5.981420 8.253830 6.732200 5.996370 18.258613 0.017985
ATTED:At1g01050.html 31 HeptamerElement:ATATAAA ATATAAA 0.08 261579_at Diurnal_Condition:LDHH_ST 18 0.884524 891.926000 581.537000 487.985000 833.646000 711.644000 766.919000 785.003000 669.036000 560.147000 803.919000 835.018000 887.773000 12.931933 67.131214
ATTED:At1g01060.html 104 | 105 | 106 HeptamerElement:ACGTGTC | HeptamerElement:CACGTGT | HeptamerElement:CCACGTG ACGTGTC | CACGTGT | CCACGTG 0.09 | 0.10 | 0.07 261569_at Diurnal_Condition:LDHH_ST 23 0.991490 2350.450000 198.731000 6.084530 5.354580 4.921860 1050.200000 2180.380000 212.766000 5.688250 3.624130 5.525280 750.085000 17.194975 478.643537
ATTED:At1g01070.html 27 | 28 | 97 HeptamerElement:ATAAATA | HeptamerElement:TATAAAT | HeptamerElement:AAAATAT ATAAATA | TATAAAT | AAAATAT 0.08 | 0.10 | 0.07 261576_at Diurnal_Condition:LDHH_ST 0 0.889697 155.449000 136.893000 27.945000 16.952400 38.159900 82.746400 235.894000 89.092900 26.519600 21.862800 76.382200 97.693900 17.898014 39.283797
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:LDHH_ST 14 0.876078 515.024000 490.063000 553.359000 702.095000 680.119000 633.018000 500.660000 537.749000 675.345000 637.940000 636.882000 625.836000 8.090339 44.290822
ATTED:At1g01090.html 32 | 33 | 34 | 35 HeptamerElement:TATATAA | HeptamerElement:ATATATA | HeptamerElement:TATATAT | HeptamerElement:ATATATA TATATAA | ATATATA | TATATAT | ATATATA 0.11 | 0.10 | 0.10 | 0.10 261583_at Diurnal_Condition:LDHH_ST 0 0.643228 1233.730000 1168.130000 1054.230000 1094.950000 1092.540000 1060.370000 1315.000000 1317.750000 1308.580000 1172.040000 1237.290000 1152.280000 20.864603 32.421805
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:LDHH_ST 20 0.755799 6966.740000 7275.200000 6782.220000 6969.110000 7677.640000 8248.570000 7269.750000 6760.510000 6259.710000 6837.320000 6924.700000 7137.070000 13.841133 237.042910
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Diurnal_Condition:LDHH_ST 15 0.930166 438.687000 189.744000 437.222000 480.107000 483.820000 487.840000 345.077000 179.540000 550.438000 459.483000 511.296000 610.922000 9.805323 63.356936
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Diurnal_Condition:LDHH_ST 7 0.641797 6.060480 5.380900 7.173910 5.854190 5.543460 6.154180 6.246300 6.962120 5.968320 5.772250 4.938180 5.264340 12.904400 0.266157
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:LDHH_ST 0 0.348577 30.932000 22.332000 31.713300 12.527700 28.187500 23.303500 9.649890 10.488500 10.996800 8.515110 8.939850 10.939000 19.021452 1.136378
ATTED:At2g26540.html 66 | 67 | 87 | 88 | 89 | 132 | 133 HeptamerElement:TTGGGCT | HeptamerElement:ATTGGGC | HeptamerElement:TTGGGCT | HeptamerElement:ATTGGGC | HeptamerElement:TATTGGG | HeptamerElement:TTGGGCC | HeptamerElement:ATTGGGC TTGGGCT | ATTGGGC | TTGGGCT | ATTGGGC | TATTGGG | TTGGGCC | ATTGGGC 0.07 | 0.08 | 0.06 | 0.08 | 0.06 | 0.07 | 0.07 245042_at Diurnal_Condition:LDHH_ST 11 0.678742 182.240000 210.704000 303.464000 294.623000 244.253000 207.139000 194.393000 254.596000 216.483000 259.336000 224.829000 290.384000 5.676939 15.926011
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Diurnal_Condition:LDHH_ST 13 0.483297 104.707000 116.641000 135.021000 135.286000 104.339000 130.665000 144.673000 105.443000 114.966000 136.328000 151.400000 132.428000 9.416274 4.327517
ATTED:At2g26560.html 27 | 28 | 29 | 30 | 176 HeptamerElement:ATAAATA | HeptamerElement:TATAAAT | HeptamerElement:CTATAAA | HeptamerElement:CCTATAA | HeptamerElement:AAAAGTC ATAAATA | TATAAAT | CTATAAA | CCTATAA | AAAAGTC 0.08 | 0.10 | 0.09 | 0.07 | 0.07 245038_at Diurnal_Condition:LDHH_ST 8 0.960600 12.928700 15.767900 176.025000 73.105400 67.819300 24.568100 7.224070 11.511100 229.630000 64.875100 21.661200 14.324200 3.437374 35.355139
ATTED:At2g26590.html 86 | 87 | 88 | 151 HeptamerElement:TGGGCTT | HeptamerElement:TTGGGCT | HeptamerElement:ATTGGGC | HeptamerElement:TTGACTT TGGGCTT | TTGGGCT | ATTGGGC | TTGACTT 0.09 | 0.06 | 0.08 | 0.06 245045_at Diurnal_Condition:LDHH_ST 11 0.674788 201.314000 224.431000 235.958000 291.344000 279.973000 212.704000 244.615000 324.313000 296.381000 248.224000 253.179000 287.296000 4.523888 9.177866
ATTED:At1g01010.html 261585_at Diurnal_Condition:LDHH_ST 12 0.808929 4.291200 5.130100 5.354110 6.632820 5.557180 4.833830 5.222210 5.696400 4.971620 6.249620 4.819030 4.690800 7.133425 0.308868
ATTED:At1g01040.html 261584_at Diurnal_Condition:LDHH_ST 22 0.340243 73.927600 56.526200 53.047100 67.687700 62.377500 70.144100 75.448800 105.247000 80.627500 70.197800 96.709800 89.578700 20.536075 2.736052
ATTED:At2g26570.html 245028_at Diurnal_Condition:LDHH_ST 12 0.319689 109.534000 115.387000 100.142000 111.373000 62.532700 114.752000 88.775800 159.312000 182.797000 114.626000 210.153000 193.073000 9.619260 2.032949
ATTED:At2g26580.html 245029_at Diurnal_Condition:LDHH_ST 17 0.879387 109.083000 143.770000 159.449000 168.904000 253.632000 174.178000 115.354000 124.980000 148.837000 151.672000 213.100000 163.862000 2.828374 22.265586
* Row count is limited to 100.