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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_8
#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 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_HIF138-8 23 0.874128 1915.000000 619.000000 784.000000 1065.000000 1254.000000 1262.000000 1935.320000 662.473000 748.120000 1000.600000 1289.200000 1143.030000 21.286403 203.213712
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_HIF138-8 0 0.992949 2931.000000 273.000000 9.000000 7.000000 8.000000 205.000000 2666.790000 295.547000 8.887250 6.385310 8.486580 189.238000 18.096075 504.210340
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_HIF138-8 16 0.858466 8.000000 7.000000 9.000000 7.000000 11.000000 7.000000 8.248810 7.615560 8.665050 6.395190 10.866900 6.924360 2.732970 0.335677
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:LIGHT5_HIF138-8 11 0.831650 156.000000 201.000000 203.000000 249.000000 175.000000 174.000000 141.773000 219.812000 202.786000 263.516000 185.575000 185.024000 4.399175 18.976022
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_HIF138-8 22 0.940157 4189.000000 3599.000000 3255.000000 3082.000000 3488.000000 3784.000000 4349.870000 3438.510000 2946.260000 2992.370000 3706.230000 3905.390000 16.368723 286.590736
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:LIGHT5_HIF138-8 20 0.659169 8019.000000 9306.000000 7821.000000 8705.000000 8486.000000 9761.000000 8704.600000 9490.490000 7193.110000 9551.720000 7800.730000 9373.950000 15.462884 188.614275
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Diurnal_Condition:LIGHT5_HIF138-8 13 0.847643 120.000000 188.000000 339.000000 277.000000 244.000000 247.000000 113.587000 180.814000 348.686000 285.965000 225.068000 243.897000 6.661512 40.429739
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Diurnal_Condition:LIGHT5_HIF138-8 22 0.833831 6.000000 5.000000 4.000000 5.000000 4.000000 6.000000 6.165050 4.839750 4.177920 5.457390 4.366070 5.709570 16.470452 0.381001
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:LIGHT5_HIF138-8 7 0.988095 6.000000 12.000000 20.000000 6.000000 7.000000 6.000000 6.127500 12.277300 18.311700 5.849120 6.639450 6.022670 0.885258 2.738177
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_HIF138-8 9 0.971128 10.000000 40.000000 54.000000 42.000000 25.000000 17.000000 10.467200 36.177700 53.111400 42.930600 23.425000 15.374700 2.982643 10.413069
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Diurnal_Condition:LIGHT5_HIF138-8 7 0.992212 26.000000 51.000000 54.000000 41.000000 21.000000 17.000000 23.886400 49.893400 52.674800 39.524100 21.646300 18.382400 1.221807 9.848242
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_HIF138-8 8 0.996699 9.000000 14.000000 75.000000 12.000000 11.000000 8.000000 8.170860 13.677700 76.255500 11.684000 10.941900 8.097440 2.018200 11.773678
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_HIF138-8 18 0.918423 200.000000 196.000000 235.000000 196.000000 288.000000 273.000000 190.896000 207.791000 235.476000 211.389000 277.587000 270.789000 10.892720 17.706296
ATTED:At1g01010.html 261585_at Diurnal_Condition:LIGHT5_HIF138-8 6 0.804729 10.000000 11.000000 11.000000 11.000000 10.000000 10.000000 9.552210 12.018400 11.696900 10.321800 10.645900 10.060500 1.578053 0.394693
ATTED:At1g01040.html 261584_at Diurnal_Condition:LIGHT5_HIF138-8 15 0.762041 41.000000 37.000000 54.000000 43.000000 57.000000 46.000000 44.996200 36.593800 49.868700 45.080700 57.287500 50.341500 9.175712 3.239500
ATTED:At2g26570.html 245028_at Diurnal_Condition:LIGHT5_HIF138-8 12 0.768087 109.000000 71.000000 106.000000 115.000000 105.000000 67.000000 101.270000 71.369200 109.243000 117.983000 114.784000 71.662100 6.027665 8.309455
ATTED:At2g26580.html 245029_at Diurnal_Condition:LIGHT5_HIF138-8 9 0.969716 83.000000 190.000000 189.000000 216.000000 137.000000 88.000000 82.841800 193.192000 191.128000 194.439000 132.710000 81.847500 3.083990 33.795087
* Row count is limited to 100.