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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_LL23_LDHH
#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
ATTED:At1g01030.html 49 | 51 | 53 | 88 HeptamerElement:TCTCTCT | HeptamerElement:TCTCTCT | HeptamerElement:TCTCTCT | HeptamerElement:ATGGGCC TCTCTCT | TCTCTCT | TCTCTCT | ATGGGCC 0.06 | 0.07 | 0.06 | 0.08 261568_at Circadian_Condition:LL23_LDHH 4 0.770875 9.759360 10.421200 7.700020 9.930560 6.861660 6.695670 6.705500 12.057600 7.864260 7.061990 7.657420 7.459510 22.752782 0.713854
ATTED:At1g01050.html 31 HeptamerElement:ATATAAA ATATAAA 0.08 261579_at Circadian_Condition:LL23_LDHH 11 0.694226 481.269000 605.769000 674.159000 566.236000 643.958000 447.524000 552.486000 523.803000 671.512000 581.275000 612.710000 589.057000 4.306310 30.614666
ATTED:At1g01060.html 104 | 105 | 106 HeptamerElement:ACGTGTC | HeptamerElement:CACGTGT | HeptamerElement:CCACGTG ACGTGTC | CACGTGT | CCACGTG 0.09 | 0.10 | 0.07 261569_at Circadian_Condition:LL23_LDHH 22 0.959876 871.413000 228.870000 12.583000 12.263500 93.303400 788.964000 771.739000 230.906000 32.537800 29.791700 206.942000 632.621000 16.401202 216.077771
ATTED:At1g01070.html 27 | 28 | 97 HeptamerElement:ATAAATA | HeptamerElement:TATAAAT | HeptamerElement:AAAATAT ATAAATA | TATAAAT | AAAATAT 0.08 | 0.10 | 0.07 261576_at Circadian_Condition:LL23_LDHH 6 0.901215 36.053800 46.490700 65.494100 30.930700 20.531700 24.694500 40.941500 48.414200 41.212300 28.522700 24.861500 25.996000 23.407541 7.708335
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Circadian_Condition:LL23_LDHH 12 0.777180 253.219000 320.561000 346.352000 340.101000 346.088000 304.251000 270.137000 313.404000 391.670000 414.358000 313.472000 363.574000 5.474513 23.471680
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 Circadian_Condition:LL23_LDHH 14 0.493701 1464.550000 1615.270000 1669.310000 1832.950000 1613.600000 1646.230000 1724.070000 1560.020000 1684.140000 1538.890000 1675.500000 1684.590000 4.837681 21.962313
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Circadian_Condition:LL23_LDHH 13 0.805386 5074.840000 5466.440000 6457.220000 6544.410000 6338.350000 5581.060000 6133.400000 5766.400000 5649.920000 7057.190000 6768.810000 5870.630000 7.073019 317.290937
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Circadian_Condition:LL23_LDHH 10 0.971305 169.783000 310.419000 356.389000 349.018000 287.479000 202.553000 190.337000 231.393000 311.582000 352.297000 304.422000 214.991000 4.703695 43.431582
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Circadian_Condition:LL23_LDHH 8 0.591197 5.483380 7.101060 7.631090 7.388960 5.529510 6.710740 6.531130 6.523850 6.699310 5.926060 6.915540 6.189710 2.149394 0.222682
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Circadian_Condition:LL23_LDHH 5 0.877207 5.387230 8.661420 7.461290 6.902310 6.354890 4.578320 6.054080 8.739890 6.656790 5.798960 5.102600 5.062270 0.222704 0.753373
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 Circadian_Condition:LL23_LDHH 11 0.580759 53.342200 116.168000 98.719400 89.803800 109.774000 83.896700 97.001300 120.192000 110.915000 100.546000 84.731200 113.471000 10.114911 4.435111
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Circadian_Condition:LL23_LDHH 16 0.626542 45.242900 42.028700 64.282100 40.452300 45.413000 56.285500 64.672200 30.571600 53.322800 55.919200 56.057800 45.225700 2.595453 1.185361
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 Circadian_Condition:LL23_LDHH 6 0.451969 6.257790 9.033200 6.077180 6.945550 7.273100 7.024800 6.679010 13.124600 15.599200 7.527780 8.195830 13.706500 12.761285 0.562059
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 Circadian_Condition:LL23_LDHH 4 0.712515 163.765000 162.062000 150.542000 129.904000 140.127000 114.401000 143.494000 131.951000 143.726000 115.637000 138.401000 99.114000 22.717534 7.356117
ATTED:At1g01010.html 261585_at Circadian_Condition:LL23_LDHH 4 0.648121 9.588530 10.904600 8.391800 8.813300 8.315230 10.655600 6.208100 10.522400 7.879910 7.248350 7.929550 7.667270 15.401757 0.359266
ATTED:At1g01040.html 261584_at Circadian_Condition:LL23_LDHH 8 0.397228 47.289900 36.140600 58.104200 36.409800 46.704200 39.797100 33.461100 35.400900 36.126400 40.938800 34.836000 45.823600 6.767898 0.501934
ATTED:At2g26570.html 245028_at Circadian_Condition:LL23_LDHH 20 0.656721 183.134000 139.674000 161.372000 145.984000 141.752000 196.148000 161.378000 107.899000 125.763000 161.297000 153.626000 139.639000 13.617620 7.635728
ATTED:At2g26580.html 245029_at Circadian_Condition:LL23_LDHH 12 0.814318 94.012600 130.869000 133.254000 199.146000 162.003000 83.117500 79.021700 115.268000 107.031000 161.243000 112.516000 112.110000 5.754162 18.711611
* Row count is limited to 100.