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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_lux_2_LDHH
#download_from http://linkdata.org/work/rdf1s288i
#namespace ATTED http://atted.jp/data/locus/
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#namespace Diurnal_Condition http://linkdata.org/work/rdf1s290i/Diurnal_condition.html#
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#namespace HeptamerElement http://linkdata.org/work/rdf1s218i/Heptamer_elements.html#
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#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:lux-2_LDHH 21 0.890207 911.327000 887.348000 797.999000 894.472000 842.865000 1012.930000 867.541000 874.157000 853.133000 829.239000 817.145000 989.743000 15.496508 29.607743
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:lux-2_LDHH 1 0.982244 662.997000 148.797000 7.940770 4.271240 4.688610 79.996100 604.855000 147.673000 7.416600 4.672660 4.520060 87.051200 18.302714 123.586541
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:lux-2_LDHH 13 0.922431 8.343410 24.402500 24.656600 27.948400 32.331700 32.063800 9.054290 22.315300 22.548100 29.050200 34.518100 30.480200 8.412250 4.336080
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:lux-2_LDHH 13 0.973977 138.258000 159.787000 217.718000 326.742000 276.616000 219.052000 130.270000 172.042000 218.214000 325.225000 293.166000 233.632000 7.604002 45.087184
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:lux-2_LDHH 21 0.973652 2328.740000 1978.910000 1484.640000 1800.780000 2141.690000 2557.830000 2427.320000 1828.930000 1343.730000 1878.860000 2240.930000 2521.020000 14.535912 258.883825
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:lux-2_LDHH 13 0.924893 6231.150000 6716.330000 7242.360000 7921.990000 7822.740000 7279.950000 6748.010000 6831.920000 7063.210000 8525.920000 7769.450000 7393.560000 7.724875 398.878370
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Diurnal_Condition:lux-2_LDHH 13 0.834261 155.758000 197.826000 252.827000 240.225000 230.844000 295.495000 149.906000 187.412000 253.469000 218.381000 223.259000 294.287000 8.811739 16.375934
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Diurnal_Condition:lux-2_LDHH 23 0.664814 5.043770 4.489360 4.238320 5.080990 4.094630 4.945810 5.092530 4.599830 4.012770 4.583020 4.272570 4.627000 16.722132 0.131820
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:lux-2_LDHH 8 0.832980 4.946760 7.760530 14.988000 7.718940 9.051540 10.608900 4.464230 7.524450 15.709300 8.183020 9.650250 10.487100 4.507244 1.171676
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:lux-2_LDHH 13 0.969977 19.611300 43.126900 62.170700 110.817000 78.746500 43.930500 21.038100 45.004100 57.895800 104.167000 81.829800 43.690100 6.578984 19.117550
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Diurnal_Condition:lux-2_LDHH 8 0.847538 22.298000 60.244100 40.071300 54.893900 36.119100 31.075000 20.665600 57.290500 41.426300 53.578200 34.456400 31.649400 2.805895 6.392329
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:lux-2_LDHH 7 0.860622 5.594580 5.498100 6.397640 5.521490 4.266150 4.662680 5.380450 5.659160 6.840550 5.015410 4.089730 4.976390 23.972946 0.461928
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:lux-2_LDHH 12 0.667208 110.942000 150.515000 135.004000 112.122000 155.334000 135.689000 100.216000 163.384000 142.628000 118.370000 160.564000 139.460000 5.925800 1.798256
ATTED:At1g01010.html 261585_at Diurnal_Condition:lux-2_LDHH 18 0.793811 6.120620 6.247050 6.911240 6.429470 7.552140 7.141410 6.223480 6.469130 6.980680 6.660970 6.956470 7.759330 1.675586 0.223306
ATTED:At1g01040.html 261584_at Diurnal_Condition:lux-2_LDHH 13 0.769732 5.575610 10.101700 12.339600 10.076400 8.021740 12.366600 5.309610 9.135540 11.613500 9.621410 7.816750 12.549500 7.176325 0.579926
ATTED:At2g26570.html 245028_at Diurnal_Condition:lux-2_LDHH 7 0.942116 108.341000 140.470000 137.941000 117.213000 107.743000 76.155500 107.141000 144.542000 148.389000 127.370000 113.531000 79.171200 1.360257 14.995055
ATTED:At2g26580.html 245029_at Diurnal_Condition:lux-2_LDHH 11 0.916401 33.558600 147.033000 141.954000 185.596000 142.821000 79.756400 33.414900 134.293000 131.043000 196.945000 156.663000 85.127400 5.225051 32.219407
* Row count is limited to 100.