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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_LER_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:LER_SD 20 0.938062 1190.420000 1003.270000 813.119000 1014.890000 1024.000000 1381.700000 1196.690000 960.049000 887.818000 1083.200000 1120.590000 1325.720000 14.286529 103.760833
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:LER_SD 23 0.980985 1956.490000 237.474000 79.548000 13.778000 31.149900 1052.670000 1905.540000 242.231000 82.560800 12.929700 33.959500 979.313000 17.052762 427.886055
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:LER_SD 20 0.989716 19.194300 8.485660 4.027270 8.799700 18.105500 26.139900 18.448500 8.399830 4.347300 8.788790 18.519100 27.683000 14.015956 5.445468
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:LER_SD 11 0.865874 215.479000 263.247000 322.043000 264.525000 299.981000 233.046000 210.688000 249.246000 346.196000 284.532000 312.896000 222.164000 4.717714 24.677204
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:LER_SD 21 0.931439 3282.770000 2704.840000 1966.010000 2586.880000 2950.270000 3261.970000 3588.450000 2861.930000 1985.880000 2444.790000 3127.050000 3247.400000 15.142497 325.495999
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:LER_SD 12 0.687767 5509.030000 5220.510000 5669.840000 5924.210000 5716.120000 5983.830000 5251.350000 5633.700000 5192.560000 6238.270000 5349.060000 5390.100000 7.770499 116.623742
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Diurnal_Condition:LER_SD 14 0.849027 147.597000 119.567000 200.349000 168.755000 209.115000 220.761000 138.484000 109.342000 185.303000 160.579000 200.326000 225.576000 10.247671 19.415884
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Diurnal_Condition:LER_SD 10 0.865224 3.178530 3.294730 4.055330 4.534550 3.556500 3.767270 3.326700 3.082540 4.206350 4.310010 3.821460 3.512110 6.018264 0.277572
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:LER_SD 12 0.891867 9.515790 8.883920 8.156510 15.726200 9.937220 12.520900 8.895230 9.485920 8.075160 16.839400 9.925040 11.569300 8.428753 1.136376
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:LER_SD 7 0.982445 35.298300 57.345500 92.810100 44.965900 38.406100 33.908600 34.978300 59.476700 86.106600 42.959100 40.198600 35.623200 1.507244 11.539036
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Diurnal_Condition:LER_SD 23 0.933456 34.127800 36.142400 29.220600 16.995000 30.828800 29.868400 34.810500 37.757600 27.405900 16.908300 30.194300 31.757400 18.587923 3.708264
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:LER_SD 12 0.914805 54.210400 35.369200 125.096000 97.129500 122.986000 68.615400 51.551300 38.859100 118.151000 95.379000 112.856000 73.112400 6.893893 18.702567
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:LER_SD 16 0.885733 201.463000 207.529000 168.754000 254.241000 261.868000 242.722000 203.542000 218.726000 159.953000 265.990000 246.514000 259.307000 10.835274 19.327005
ATTED:At1g01010.html 261585_at Diurnal_Condition:LER_SD 18 0.931844 8.141490 6.195630 5.518210 7.888650 7.541100 8.900510 8.071670 6.439250 5.358950 7.871170 8.022520 8.492750 13.024070 0.706875
ATTED:At1g01040.html 261584_at Diurnal_Condition:LER_SD 20 0.966753 26.335500 24.270900 19.179900 22.085600 31.493200 34.708600 27.653100 23.408300 17.526800 22.656400 28.472900 32.756100 13.758125 3.467345
ATTED:At2g26570.html 245028_at Diurnal_Condition:LER_SD 1 0.950077 255.321000 247.220000 150.238000 99.164400 128.544000 160.709000 236.471000 245.547000 143.074000 91.885100 136.558000 156.834000 19.495704 38.469308
ATTED:At2g26580.html 245029_at Diurnal_Condition:LER_SD 7 0.944574 58.338400 100.167000 131.362000 84.717200 74.815900 77.084400 59.958700 93.740200 129.098000 77.880400 72.085300 78.625300 1.940500 12.535150
* Row count is limited to 100.