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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_LIGHT5_HIF138_13
#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#
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#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:LIGHT5_HIF138-13 23 0.857290 1915.000000 619.000000 784.000000 1065.000000 1254.000000 1262.000000 1959.650000 593.606000 772.441000 1078.280000 1356.120000 1268.610000 21.566831 212.918553
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:LIGHT5_HIF138-13 0 0.994051 2931.000000 273.000000 9.000000 7.000000 8.000000 205.000000 2724.310000 263.199000 8.714710 6.932480 7.499720 195.727000 18.074740 507.866660
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:LIGHT5_HIF138-13 16 0.902119 8.000000 7.000000 9.000000 7.000000 11.000000 7.000000 8.297800 7.576380 8.225920 7.525810 11.140700 6.988500 2.938730 0.434696
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:LIGHT5_HIF138-13 11 0.913450 156.000000 201.000000 203.000000 249.000000 175.000000 174.000000 171.436000 190.655000 187.155000 266.401000 159.657000 187.121000 4.454508 15.772077
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:LIGHT5_HIF138-13 23 0.933326 4189.000000 3599.000000 3255.000000 3082.000000 3488.000000 3784.000000 4412.820000 3869.950000 2966.200000 3262.010000 3627.480000 3948.110000 16.837071 278.648157
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:LIGHT5_HIF138-13 20 0.545326 8019.000000 9306.000000 7821.000000 8705.000000 8486.000000 9761.000000 8094.890000 9265.300000 7978.210000 8947.510000 8213.830000 8917.500000 14.919492 100.759035
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Diurnal_Condition:LIGHT5_HIF138-13 13 0.880506 120.000000 188.000000 339.000000 277.000000 244.000000 247.000000 113.818000 177.173000 325.431000 264.654000 250.018000 246.859000 5.698945 38.247442
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Diurnal_Condition:LIGHT5_HIF138-13 22 0.839360 6.000000 5.000000 4.000000 5.000000 4.000000 6.000000 5.765190 5.098690 3.682770 4.930080 3.796970 6.492940 16.536835 0.484358
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:LIGHT5_HIF138-13 7 0.990602 6.000000 12.000000 20.000000 6.000000 7.000000 6.000000 6.251890 12.978500 21.985500 5.483320 6.657200 6.519420 0.881938 3.023819
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:LIGHT5_HIF138-13 9 0.959440 10.000000 40.000000 54.000000 42.000000 25.000000 17.000000 10.498200 40.008200 55.058200 40.978000 26.383100 18.077500 2.918760 10.256360
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Diurnal_Condition:LIGHT5_HIF138-13 7 0.991606 26.000000 51.000000 54.000000 41.000000 21.000000 17.000000 23.715500 52.447800 54.676200 39.462900 20.933200 17.855800 1.165071 10.239596
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:LIGHT5_HIF138-13 8 0.995523 9.000000 14.000000 75.000000 12.000000 11.000000 8.000000 8.817500 14.645500 80.081900 12.552400 10.853700 7.745300 1.998712 12.174997
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:LIGHT5_HIF138-13 18 0.850960 200.000000 196.000000 235.000000 196.000000 288.000000 273.000000 198.743000 184.567000 246.603000 212.718000 271.995000 250.664000 1.486486 17.276387
ATTED:At1g01010.html 261585_at Diurnal_Condition:LIGHT5_HIF138-13 6 0.741880 10.000000 11.000000 11.000000 11.000000 10.000000 10.000000 10.930200 11.290800 10.140500 10.524900 9.921600 9.024980 0.457924 0.325997
ATTED:At1g01040.html 261584_at Diurnal_Condition:LIGHT5_HIF138-13 14 0.810649 41.000000 37.000000 54.000000 43.000000 57.000000 46.000000 38.046700 34.786900 53.628600 45.403100 54.203000 46.975300 8.034052 3.519992
ATTED:At2g26570.html 245028_at Diurnal_Condition:LIGHT5_HIF138-13 8 0.655340 109.000000 71.000000 106.000000 115.000000 105.000000 67.000000 117.194000 66.166200 99.528300 117.509000 103.303000 61.679400 5.765009 6.705005
ATTED:At2g26580.html 245029_at Diurnal_Condition:LIGHT5_HIF138-13 9 0.973506 83.000000 190.000000 189.000000 216.000000 137.000000 88.000000 80.482500 204.726000 200.909000 217.564000 131.057000 91.582200 3.126886 35.596380
* Row count is limited to 100.