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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_shortday
#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 Diurnal_Condition:shortday 16 0.480706 9.364150 8.479960 11.766400 10.152100 8.137180 8.378090 9.666940 6.544100 7.465120 8.644470 10.717000 8.541870 4.341623 0.260531
ATTED:At1g01050.html 31 HeptamerElement:ATATAAA ATATAAA 0.08 261579_at Diurnal_Condition:shortday 19 0.969702 1042.790000 883.745000 666.806000 955.825000 1191.890000 1211.470000 1017.890000 859.831000 724.969000 892.205000 1045.060000 1217.080000 13.338513 117.574219
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:shortday 23 0.971688 2065.290000 46.737100 6.004850 4.667040 15.580800 894.616000 2132.100000 56.973700 3.928000 6.220940 18.281700 1398.790000 19.311291 474.624236
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:shortday 22 0.913098 91.799300 25.047500 12.018800 51.061100 41.121800 123.573000 90.788300 32.625700 23.501900 32.350400 57.516500 94.854700 14.751334 21.495971
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:shortday 11 0.893387 365.220000 346.955000 524.017000 454.433000 391.970000 325.899000 332.544000 352.351000 514.671000 421.563000 425.291000 300.972000 4.008690 42.583229
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:shortday 20 0.884253 2878.560000 2221.820000 1752.820000 2216.330000 2699.250000 2532.970000 2919.500000 2239.430000 1575.970000 2427.050000 2574.660000 2994.150000 14.354539 266.313011
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:shortday 17 0.602618 6195.310000 6678.310000 6905.870000 6375.970000 7565.760000 6663.480000 6135.610000 5943.640000 6736.700000 6259.280000 6569.710000 6848.480000 2.882948 137.009117
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Diurnal_Condition:shortday 15 0.940196 253.163000 225.413000 374.445000 443.816000 512.505000 478.334000 236.476000 252.375000 426.100000 468.403000 530.415000 397.903000 8.649940 72.326461
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Diurnal_Condition:shortday 5 0.625600 4.290250 5.018700 4.680470 4.240260 4.644670 4.975670 4.104860 4.877910 4.660750 4.557760 3.928160 4.470520 22.903975 0.091710
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:shortday 12 0.894908 8.275370 7.367550 5.862400 16.764500 10.220400 11.639800 10.207900 7.636170 10.251400 24.320700 9.143280 9.458300 7.330239 1.976107
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:shortday 7 0.952805 50.233800 96.320200 120.295000 55.340500 30.310500 30.165800 46.869000 73.995200 138.497000 46.794000 43.627800 47.918800 0.741811 20.379968
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Diurnal_Condition:shortday 3 0.853318 64.438000 75.586900 60.299800 41.532100 35.920600 46.790700 76.048200 86.003100 69.286400 37.130900 63.722100 49.221600 21.161465 9.361835
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:shortday 11 0.704372 15.517400 19.143200 21.047700 23.877900 18.104000 14.805900 20.355000 25.715500 38.720200 79.620500 21.028400 15.309400 4.596337 7.106913
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:shortday 21 0.844038 307.377000 252.253000 137.479000 236.690000 273.047000 323.155000 249.341000 278.743000 211.252000 200.016000 273.719000 290.107000 15.012896 28.705180
ATTED:At1g01010.html 261585_at Diurnal_Condition:shortday 0 0.662081 7.521850 10.002600 7.203440 6.967450 7.707640 12.978600 11.782800 12.811900 7.862520 9.668000 9.416520 9.995370 17.235582 0.805100
ATTED:At1g01040.html 261584_at Diurnal_Condition:shortday 22 0.860422 71.987000 71.783600 48.889500 50.314400 43.902700 81.486500 80.784000 53.350500 46.284100 61.031400 59.122600 80.366700 16.385531 7.841701
ATTED:At2g26570.html 245028_at Diurnal_Condition:shortday 2 0.879550 257.282000 337.766000 143.400000 135.476000 199.270000 187.955000 357.393000 435.448000 191.595000 107.511000 165.499000 210.188000 19.747257 56.424724
ATTED:At2g26580.html 245029_at Diurnal_Condition:shortday 12 0.718985 26.803400 31.323100 103.546000 58.799700 70.486300 62.207800 42.404500 51.235300 79.024300 53.415100 74.752900 49.264600 5.747009 9.178145
* Row count is limited to 100.