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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_longday
#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:longday 21 0.893647 911.954000 905.839000 780.149000 852.598000 886.386000 1027.270000 951.886000 933.616000 764.554000 886.320000 875.965000 1011.300000 15.244695 45.544763
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:longday 1 0.986737 2243.220000 481.200000 7.198880 4.786970 10.671700 150.279000 1904.970000 483.612000 8.462220 6.001530 10.889400 135.684000 18.466888 398.319989
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:longday 0 0.903148 81.802000 59.126300 54.982500 24.269300 47.658000 76.836400 86.856000 91.586300 58.462100 42.639200 52.335600 68.620600 18.430553 12.002434
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:longday 15 0.970304 382.839000 363.731000 345.336000 435.663000 542.594000 395.455000 385.821000 361.562000 341.571000 424.496000 558.009000 392.072000 10.064003 39.286307
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:longday 3 0.914181 2359.530000 2579.170000 2092.310000 1848.720000 1711.330000 2064.460000 2527.810000 2187.500000 1864.000000 1890.110000 1712.150000 2119.670000 19.769314 180.151397
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:longday 19 0.815166 6029.510000 4981.260000 5422.640000 5800.940000 6558.730000 6207.380000 5667.670000 4233.800000 4723.740000 5121.320000 5685.040000 5895.260000 12.210979 360.308700
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Diurnal_Condition:longday 15 0.917319 351.982000 186.230000 367.941000 468.625000 380.768000 488.027000 318.968000 235.761000 432.241000 427.566000 462.719000 468.322000 9.627945 51.259637
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Diurnal_Condition:longday 17 0.539075 4.732650 4.850910 6.282960 5.047300 6.033100 5.230630 5.392090 4.967900 5.346920 4.799960 5.711780 5.571210 3.276431 0.121144
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:longday 8 0.670834 8.767370 9.762920 10.981300 10.071500 9.198180 9.825390 12.101700 8.553420 17.239000 10.986300 5.901360 10.899000 11.060797 0.797098
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:longday 11 0.836888 56.214400 85.982900 127.953000 116.882000 131.628000 52.777500 53.255000 87.920600 132.786000 78.975400 91.971600 60.416800 4.359387 16.957641
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Diurnal_Condition:longday 23 0.663723 63.188600 68.963800 62.358000 61.684500 60.304500 60.590600 63.663900 61.908700 60.446500 45.385300 71.443700 69.274100 16.885154 1.990424
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:longday 8 0.914366 10.820000 9.568140 38.233200 14.602400 15.050200 16.381600 13.851100 12.681000 52.805600 22.531100 16.388500 23.712100 3.308453 4.652077
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:longday 21 0.868286 252.231000 218.992000 216.603000 187.201000 232.966000 248.322000 232.512000 189.098000 178.521000 180.067000 250.998000 229.461000 14.757289 15.243051
ATTED:At1g01010.html 261585_at Diurnal_Condition:longday 23 0.840829 11.264600 8.808780 8.567640 9.250020 8.789070 13.117100 11.002200 9.957570 9.663360 8.075890 8.433150 9.962780 16.708184 0.718835
ATTED:At1g01040.html 261584_at Diurnal_Condition:longday 22 0.599625 77.339200 55.941700 36.103600 46.850800 55.825300 58.782000 49.973100 51.572900 63.408500 42.904300 57.669800 63.764200 16.093233 4.374103
ATTED:At2g26570.html 245028_at Diurnal_Condition:longday 3 0.968870 254.631000 401.577000 188.126000 188.754000 231.408000 174.591000 237.830000 385.896000 181.071000 184.942000 182.743000 140.585000 21.536411 38.593476
ATTED:At2g26580.html 245029_at Diurnal_Condition:longday 16 0.976838 50.030200 27.857600 59.220500 74.527100 94.364200 72.517100 45.733400 24.313900 43.072000 77.617300 105.582000 85.485800 9.989120 16.985094
* Row count is limited to 100.