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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_LL_LDHC
#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:LL_LDHC 21 0.620469 6.937120 7.707960 4.872600 8.613070 8.300830 9.034470 8.871380 5.775550 9.759090 5.500730 5.655960 11.596100 14.566265 0.596785
ATTED:At1g01050.html 31 HeptamerElement:ATATAAA ATATAAA 0.08 261579_at Circadian_Condition:LL_LDHC 21 0.726582 1032.550000 640.031000 492.383000 695.271000 818.403000 893.336000 800.310000 861.088000 625.708000 666.779000 879.020000 715.899000 15.072014 71.523446
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:LL_LDHC 1 0.919990 2034.060000 483.085000 4.838540 3.973530 8.879690 125.197000 982.028000 699.693000 131.125000 9.150800 8.603460 202.681000 18.859784 314.736964
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:LL_LDHC 0 0.569027 14.165900 8.934570 6.637720 6.618780 6.311630 13.766300 11.288400 14.948200 7.858570 14.542200 8.869480 9.422000 18.002457 1.082513
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Circadian_Condition:LL_LDHC 17 0.867406 471.479000 375.287000 393.742000 520.105000 584.361000 489.953000 453.469000 473.246000 418.422000 508.309000 609.143000 495.726000 10.476802 40.604390
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:LL_LDHC 5 0.778906 2390.570000 2426.260000 2123.270000 1984.000000 1598.280000 1790.730000 2097.190000 1988.660000 2153.130000 2392.940000 1757.300000 2048.350000 22.798170 113.588375
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Circadian_Condition:LL_LDHC 14 0.897362 6455.990000 6449.150000 6685.860000 7431.460000 7815.120000 6363.230000 6100.370000 5507.000000 5837.890000 6737.980000 7881.900000 7586.800000 9.882572 438.586405
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Circadian_Condition:LL_LDHC 15 0.830159 223.536000 130.885000 336.099000 264.563000 269.513000 383.440000 292.019000 112.469000 251.780000 350.055000 289.538000 238.730000 9.443617 32.205550
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Circadian_Condition:LL_LDHC 5 0.830733 6.823370 10.444300 9.107370 6.675870 5.231860 6.084960 6.180470 8.292490 6.548200 6.047140 5.514450 6.243340 23.005041 0.845303
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Circadian_Condition:LL_LDHC 7 0.847580 22.383800 50.137300 41.083600 26.949900 8.402560 6.664980 7.552770 9.993950 23.152900 33.223500 18.665400 11.343600 1.879982 6.493037
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:LL_LDHC 12 0.346588 55.970800 32.308800 73.491500 89.154300 113.893000 158.738000 75.789600 196.272000 105.953000 123.952000 134.488000 53.333000 8.080819 7.301225
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Circadian_Condition:LL_LDHC 18 0.436992 52.122500 51.836900 49.133300 50.454100 43.495400 58.423400 38.580700 37.423000 58.746700 46.754500 67.725900 43.993100 3.650121 2.063063
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:LL_LDHC 7 0.507040 17.634000 32.915600 82.267600 25.977200 11.822200 9.542160 5.840110 9.094060 16.795600 18.083700 10.680200 76.869000 2.109180 2.726035
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:LL_LDHC 16 0.297893 311.659000 250.399000 274.827000 267.329000 266.251000 260.011000 141.289000 176.187000 234.870000 166.758000 240.152000 185.994000 5.014036 4.558824
ATTED:At1g01010.html 261585_at Circadian_Condition:LL_LDHC 23 0.717176 6.799680 11.841300 5.947740 6.112530 5.635640 8.570000 10.512800 6.603250 5.918020 6.503490 8.307980 6.759010 18.394124 0.727079
ATTED:At1g01040.html 261584_at Circadian_Condition:LL_LDHC 19 0.865186 36.362400 31.466100 39.954900 37.573100 37.091200 57.251000 41.913700 34.646700 41.034400 41.101700 56.226200 72.291300 23.406578 5.533984
ATTED:At2g26570.html 245028_at Circadian_Condition:LL_LDHC 8 0.623915 195.686000 176.341000 280.691000 199.670000 164.555000 168.102000 118.969000 258.888000 172.547000 179.974000 181.327000 129.095000 1.655430 19.513425
ATTED:At2g26580.html 245029_at Circadian_Condition:LL_LDHC 11 0.790187 87.774600 103.213000 261.621000 272.774000 151.547000 66.767700 131.170000 76.335600 95.264800 152.537000 211.044000 147.371000 6.359911 30.908869
* Row count is limited to 100.