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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_phyB9_SD
#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:phyB9_SD 19 0.937053 1061.990000 767.687000 759.285000 927.991000 1081.230000 1406.560000 1071.880000 693.272000 746.505000 933.155000 1123.520000 1540.200000 13.211942 165.955063
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:phyB9_SD 22 0.957800 1095.230000 172.653000 3.829100 5.230700 164.188000 1779.490000 1143.510000 173.185000 3.627170 4.731470 158.104000 1676.400000 15.546658 412.620141
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:phyB9_SD 0 0.952142 47.842800 12.485300 7.713270 8.567800 20.158900 11.331200 46.031300 13.377300 7.085180 7.728370 20.052900 10.229600 17.072196 6.334663
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:phyB9_SD 10 0.949332 63.447100 123.332000 289.635000 267.867000 132.977000 135.539000 69.179600 125.947000 314.362000 271.095000 131.095000 148.063000 4.349593 52.667674
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:phyB9_SD 20 0.985458 2891.650000 2397.360000 1870.550000 2433.200000 2831.130000 3140.880000 2810.790000 2351.590000 1701.140000 2378.750000 2877.320000 3274.660000 13.939434 314.109902
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:phyB9_SD 16 0.884984 5625.140000 5468.620000 5551.560000 6612.580000 5874.640000 6329.980000 5425.600000 5015.150000 5539.830000 6285.000000 6337.290000 6083.860000 9.479618 278.648968
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Diurnal_Condition:phyB9_SD 17 0.832322 150.865000 136.890000 214.094000 148.256000 265.891000 184.632000 161.416000 145.680000 212.688000 152.891000 264.939000 180.477000 2.778179 18.027529
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Diurnal_Condition:phyB9_SD 12 0.804840 3.200970 3.750790 4.108090 3.850180 3.599840 4.281760 3.229930 3.903790 3.746690 4.177880 3.732640 4.038430 6.392549 0.100816
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:phyB9_SD 21 0.736565 41.396300 34.616200 10.159000 28.475200 38.951800 18.392700 41.347100 34.626500 9.681710 26.938300 41.310200 16.609300 15.490781 3.093991
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:phyB9_SD 7 0.975305 20.884900 41.552500 78.831900 32.661600 23.538200 31.017700 19.644000 45.213200 80.538000 30.014600 23.698800 34.019600 1.542845 10.506038
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Diurnal_Condition:phyB9_SD 11 0.876133 15.976400 12.618600 18.983800 21.467000 11.844200 14.934500 16.564900 13.440800 17.468000 22.713800 10.761700 14.699800 8.248772 1.334849
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:phyB9_SD 13 0.906128 195.820000 50.136900 83.874100 362.434000 192.511000 95.644100 178.673000 50.909000 81.704700 334.688000 183.076000 102.190000 8.060643 43.102472
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:phyB9_SD 4 0.814320 202.989000 276.861000 195.004000 245.707000 210.077000 217.483000 222.102000 283.785000 183.667000 239.568000 198.273000 229.778000 21.684406 7.350826
ATTED:At1g01010.html 261585_at Diurnal_Condition:phyB9_SD 16 0.989417 8.752670 9.321970 9.175190 8.932910 20.383100 10.935700 9.512160 8.635880 8.915930 9.034290 20.978300 10.087200 10.430312 2.073194
ATTED:At1g01040.html 261584_at Diurnal_Condition:phyB9_SD 16 0.879273 25.835900 13.465100 21.849100 19.800500 23.579700 24.048300 23.585900 12.816900 20.809500 18.692600 22.331900 22.161700 12.546052 1.690186
ATTED:At2g26570.html 245028_at Diurnal_Condition:phyB9_SD 1 0.944067 158.448000 211.858000 102.252000 65.704900 96.844200 157.565000 162.450000 191.459000 104.345000 59.701400 89.641200 151.467000 19.039179 30.723758
ATTED:At2g26580.html 245029_at Diurnal_Condition:phyB9_SD 8 0.924888 60.233500 129.301000 105.674000 116.750000 53.315000 78.193200 56.831300 140.532000 104.776000 114.490000 51.010700 74.081100 1.156457 16.912140
* Row count is limited to 100.