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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_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
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ATTED:At1g01050.html 31 HeptamerElement:ATATAAA ATATAAA 0.08 261579_at Diurnal_Condition:COL_LDHH 19 0.992415 1102.340000 779.917000 619.206000 938.200000 1143.050000 1298.090000 1047.550000 784.906000 618.378000 922.992000 1248.500000 1336.120000 13.106005 167.426298
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_LDHH 0 0.992101 2365.880000 254.607000 5.411850 6.313510 5.597350 238.476000 2317.800000 230.181000 5.410650 5.995790 5.466460 239.345000 18.004327 428.477945
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_LDHH 21 0.968451 31.088600 25.122500 7.622910 18.684000 24.677000 39.047300 29.166800 24.211200 7.366660 17.938400 26.029800 39.300500 14.950536 6.522696
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:COL_LDHH 14 0.886510 200.896000 171.189000 147.380000 259.428000 284.702000 213.399000 210.301000 172.523000 151.164000 261.698000 297.045000 206.965000 10.111113 29.504941
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_LDHH 21 0.919473 2791.550000 1968.440000 1394.630000 2039.240000 2310.120000 2485.890000 2773.230000 2026.850000 1524.090000 1840.060000 2388.230000 2469.610000 14.983484 278.432440
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:COL_LDHH 18 0.827587 6489.440000 6273.760000 7137.650000 6786.710000 7926.200000 7704.840000 6734.490000 6384.260000 7325.950000 7235.320000 7646.410000 7825.090000 1.769621 321.151025
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Diurnal_Condition:COL_LDHH 15 0.963962 152.968000 109.508000 192.272000 250.136000 256.798000 233.577000 163.408000 114.319000 177.807000 242.018000 240.162000 240.509000 9.429458 34.806346
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Diurnal_Condition:COL_LDHH 22 0.902376 6.477380 4.925220 4.788700 4.824460 4.153480 6.170910 6.292050 4.742730 5.024020 5.187210 3.977040 5.931960 17.470411 0.393068
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:COL_LDHH 16 0.929266 8.967260 5.242190 6.003050 11.851900 16.913800 10.431800 9.758070 5.631530 6.542940 10.823900 15.499600 9.696500 10.438046 2.290551
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_LDHH 14 0.969245 51.318600 37.538700 35.358800 102.779000 93.044200 45.318600 55.163600 39.110200 37.510800 93.121500 92.850700 49.007300 8.688894 14.573738
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Diurnal_Condition:COL_LDHH 12 0.788027 30.843900 46.783300 38.439300 38.136400 45.180700 46.911700 32.332900 45.177400 41.118000 37.109900 45.037600 44.042500 9.777553 0.833980
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_LDHH 16 0.848409 5.075250 4.406430 5.103430 4.676740 6.121320 4.555300 5.286960 4.370130 5.555090 4.739550 6.620270 4.814160 9.602814 0.238584
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_LDHH 19 0.941378 146.364000 125.042000 106.378000 149.161000 165.211000 191.444000 153.973000 120.448000 100.260000 163.744000 157.478000 196.553000 23.332849 18.948098
ATTED:At1g01010.html 261585_at Diurnal_Condition:COL_LDHH 20 0.679210 9.821790 6.419780 7.227200 5.807330 9.147150 6.811280 10.262200 6.855390 7.474120 5.437970 9.719590 6.501230 15.717627 0.539121
ATTED:At1g01040.html 261584_at Diurnal_Condition:COL_LDHH 19 0.814782 12.397900 9.904870 7.400820 13.089800 10.530200 10.025400 13.467500 9.341410 7.675150 12.924300 10.432500 10.655100 13.054047 0.549119
ATTED:At2g26570.html 245028_at Diurnal_Condition:COL_LDHH 20 0.817279 114.000000 118.847000 88.100400 119.296000 114.550000 99.435000 102.707000 116.464000 79.500400 129.018000 113.298000 105.822000 1.272396 2.305756
ATTED:At2g26580.html 245029_at Diurnal_Condition:COL_LDHH 11 0.954350 83.502900 109.325000 156.652000 207.553000 134.853000 86.772200 82.073600 98.780300 150.180000 214.188000 145.418000 93.761100 5.499031 29.872949
* Row count is limited to 100.