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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_COL_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#
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#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:COL_SD 19 0.961095 1083.200000 791.712000 825.803000 887.351000 1060.420000 1133.900000 1078.970000 723.049000 749.221000 949.804000 1149.870000 1109.980000 12.985121 101.833992
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:COL_SD 23 0.964826 2182.180000 154.113000 4.678410 3.399820 8.216240 1325.480000 2174.700000 139.181000 4.584960 3.608250 7.768750 1355.820000 19.306590 515.228926
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:COL_SD 23 0.914464 15.136000 7.431320 4.204370 8.038850 5.618450 8.431320 15.028400 7.785940 3.880130 8.593850 5.499450 9.049210 17.150306 1.732642
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:COL_SD 11 0.970719 187.089000 240.130000 277.880000 305.676000 267.416000 187.195000 204.499000 219.613000 304.720000 316.931000 261.319000 178.669000 4.740537 32.930874
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:COL_SD 19 0.932624 2545.930000 2112.010000 1655.140000 2289.950000 2784.060000 2678.370000 2301.850000 1986.010000 1690.690000 2225.710000 2659.900000 2431.180000 12.757270 228.904104
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:COL_SD 16 0.817251 5842.460000 5469.760000 5944.710000 6121.760000 6650.750000 5875.020000 5995.650000 5103.660000 5529.700000 5754.320000 6048.670000 6175.940000 10.723415 206.463367
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Diurnal_Condition:COL_SD 14 0.981365 118.870000 105.491000 190.522000 200.496000 190.588000 186.950000 108.819000 96.463500 198.309000 190.458000 183.102000 175.943000 7.714792 24.244130
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Diurnal_Condition:COL_SD 0 0.884827 3.643540 3.711540 4.129690 2.832740 3.695100 3.784520 3.417180 3.782900 3.974430 2.707760 3.903830 3.452820 20.169447 0.102272
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:COL_SD 19 0.810437 57.878100 42.028100 14.079400 54.669700 63.558100 30.889800 54.758700 43.871000 13.242000 52.611700 62.532000 32.189700 12.182152 5.487393
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:COL_SD 12 0.927867 26.373100 64.506000 64.995700 51.798900 61.187500 65.628700 25.941500 65.281300 71.157800 52.347700 66.826000 59.173300 6.756763 4.812546
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Diurnal_Condition:COL_SD 11 0.846300 19.232900 18.922600 26.092800 20.716000 23.061600 16.369200 17.818900 20.040800 28.442400 22.666100 25.185200 16.310400 4.237665 2.038086
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:COL_SD 14 0.968824 84.942100 59.116400 154.165000 454.318000 392.966000 139.485000 80.970200 57.855800 150.385000 492.799000 412.740000 150.677000 7.818233 106.203898
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:COL_SD 21 0.841237 204.989000 256.673000 148.020000 219.513000 224.095000 212.314000 209.090000 269.027000 148.017000 201.885000 239.673000 214.235000 15.750329 8.909715
ATTED:At1g01010.html 261585_at Diurnal_Condition:COL_SD 21 0.966409 14.929500 10.661400 6.817990 8.232170 9.684890 22.494500 15.759300 9.831570 6.304860 7.697880 10.083500 24.039800 15.223278 3.549517
ATTED:At1g01040.html 261584_at Diurnal_Condition:COL_SD 14 0.857403 17.536800 15.734100 17.685400 22.362400 21.883000 16.467900 19.116400 14.508300 19.332100 21.102400 21.870700 15.260600 7.580841 1.475554
ATTED:At2g26570.html 245028_at Diurnal_Condition:COL_SD 3 0.949885 131.215000 201.366000 81.110200 89.534700 113.626000 104.927000 141.085000 191.822000 80.192700 87.360600 117.761000 109.451000 16.339955 18.635982
ATTED:At2g26580.html 245029_at Diurnal_Condition:COL_SD 10 0.867640 88.440100 153.912000 159.132000 114.461000 142.783000 93.253800 96.550900 147.508000 167.892000 119.135000 149.896000 84.498500 2.731974 15.105226
* Row count is limited to 100.