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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
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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_SM
#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
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ATTED:At1g01050.html 31 HeptamerElement:ATATAAA ATATAAA 0.08 261579_at Diurnal_Condition:LDHH_SM 20 0.843471 1215.190000 809.264000 697.388000 728.289000 907.040000 1045.530000 1086.050000 761.092000 750.864000 1091.380000 975.495000 1147.350000 14.488207 95.907556
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_SM 0 0.983276 2766.660000 499.938000 7.138490 5.708520 4.777820 449.045000 3021.050000 385.109000 10.042000 5.298470 5.571880 222.034000 18.111633 545.316276
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_SM 1 0.571718 24.236400 12.814400 10.145500 5.129350 7.166690 7.694510 5.216210 10.454400 4.630850 7.559070 10.724400 13.750000 18.187183 1.901209
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:LDHH_SM 13 0.701176 476.592000 485.682000 461.091000 623.458000 542.669000 502.536000 380.111000 464.892000 502.198000 534.646000 469.808000 533.411000 7.432512 26.511254
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_SM 0 0.623843 1328.940000 1392.810000 1270.450000 1467.500000 1274.230000 1481.220000 1467.330000 1506.940000 1235.640000 1261.940000 1358.180000 1378.550000 17.252775 32.056420
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:LDHH_SM 18 0.842815 7912.030000 7141.830000 6452.110000 7846.070000 7842.920000 8242.740000 6940.750000 6823.630000 7365.220000 7332.760000 8031.510000 7969.210000 11.914719 310.662281
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Diurnal_Condition:LDHH_SM 16 0.807616 326.491000 159.053000 293.927000 291.123000 301.807000 302.691000 254.575000 117.629000 232.782000 207.198000 257.135000 353.389000 12.067503 29.711548
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Diurnal_Condition:LDHH_SM 1 0.671284 6.565620 6.114850 5.986900 6.281700 6.520690 5.708040 7.469530 6.567390 6.068790 6.782970 5.810120 5.683270 21.148121 0.099879
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:LDHH_SM 4 0.551043 152.555000 69.379700 87.923100 21.170700 37.955400 39.532400 43.591100 65.559200 83.087900 18.636700 97.694000 47.031600 15.832262 11.242336
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_SM 6 0.362899 91.489100 146.233000 140.489000 97.982400 96.414300 128.625000 80.255200 75.204700 84.507000 65.171100 96.966100 82.642700 13.568493 3.289036
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Diurnal_Condition:LDHH_SM 11 0.623331 37.613400 51.868800 48.448800 78.391600 75.805300 36.068200 41.262100 74.747900 45.718500 43.422900 33.002500 54.456600 7.825959 3.365223
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_SM 8 0.915399 75.830800 40.287100 829.596000 406.542000 339.878000 173.349000 44.464300 391.342000 1137.990000 266.823000 187.783000 66.090000 3.068603 169.651229
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_SM 20 0.759194 183.652000 169.616000 156.603000 148.748000 199.141000 194.130000 155.610000 138.045000 142.986000 104.380000 197.481000 178.900000 13.941916 13.417260
ATTED:At1g01010.html 261585_at Diurnal_Condition:LDHH_SM 16 0.573100 9.708080 7.268090 7.273990 6.533070 8.062720 7.269570 5.786590 9.728710 6.539650 7.305240 12.416700 8.095140 12.600119 0.367805
ATTED:At1g01040.html 261584_at Diurnal_Condition:LDHH_SM 1 0.735504 105.774000 82.634800 46.378500 93.421000 86.082500 75.409700 211.141000 110.464000 96.981600 82.632300 80.197400 90.852900 17.921836 13.813092
ATTED:At2g26570.html 245028_at Diurnal_Condition:LDHH_SM 5 0.648925 260.316000 333.077000 307.283000 240.308000 176.091000 184.075000 252.381000 263.909000 160.893000 267.090000 184.030000 277.327000 13.979913 20.242072
ATTED:At2g26580.html 245029_at Diurnal_Condition:LDHH_SM 15 0.790556 258.860000 223.316000 324.990000 368.350000 409.517000 404.065000 264.198000 195.234000 336.238000 279.439000 350.155000 285.237000 9.244223 35.486073
* Row count is limited to 100.