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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_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 Diurnal_Condition:LDHC 18 0.743106 8.104670 8.306040 7.882450 7.629650 9.204070 9.093820 9.395080 8.005800 8.898930 7.900130 10.688000 12.229500 13.280642 0.620729
ATTED:At1g01050.html 31 HeptamerElement:ATATAAA ATATAAA 0.08 261579_at Diurnal_Condition:LDHC 23 0.873643 865.066000 561.266000 487.413000 590.691000 682.420000 760.905000 1050.400000 696.231000 595.639000 681.137000 669.443000 796.714000 15.961226 80.703652
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:LDHC 23 0.975758 2829.800000 455.767000 6.507330 4.340080 4.552510 775.053000 2305.150000 421.857000 4.645480 3.920110 5.004530 704.438000 17.685271 526.360105
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:LDHC 3 0.807961 17.414800 16.255400 10.608100 5.038850 7.977150 6.631470 17.062000 8.907300 13.134900 7.023690 6.698480 12.136300 19.867557 2.375877
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:LDHC 12 0.794410 307.366000 320.192000 364.904000 510.382000 229.839000 391.323000 261.345000 362.749000 332.879000 508.143000 333.875000 424.624000 5.989380 27.593315
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:LDHC 1 0.836233 2632.930000 2951.520000 2410.490000 2192.300000 2658.370000 2809.580000 3030.560000 2673.220000 2524.370000 2408.810000 2473.850000 2833.000000 18.426416 139.409457
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:LDHC 18 0.845971 6835.500000 6141.950000 6310.520000 7145.280000 6623.230000 7269.060000 6597.060000 5794.310000 5774.820000 6536.400000 6850.990000 6697.550000 11.900097 246.846096
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Diurnal_Condition:LDHC 15 0.910758 216.195000 159.109000 409.694000 377.929000 335.976000 393.314000 311.106000 177.753000 366.121000 359.784000 320.842000 334.984000 8.060329 38.280788
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Diurnal_Condition:LDHC 4 0.465957 5.729030 7.628500 6.054150 5.843090 7.609300 5.700210 6.108320 6.333330 5.306520 6.896170 5.734060 5.626960 3.145693 0.069232
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:LDHC 0 0.579199 47.861600 65.508100 127.752000 22.097000 57.617600 77.016800 70.651500 76.414800 58.746000 38.919200 113.854000 50.945100 22.120715 2.373502
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:LDHC 11 0.860746 52.327700 98.030800 96.090400 154.148000 87.499600 75.416800 71.202400 132.426000 178.733000 114.753000 76.667400 100.193000 8.768686 18.014922
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Diurnal_Condition:LDHC 19 0.540273 45.941500 36.042700 60.499800 35.887400 53.289300 50.226900 41.272700 41.249700 46.302400 47.941700 41.026900 63.805200 0.274463 1.754888
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:LDHC 23 0.693871 222.568000 21.163200 216.452000 25.297100 82.705400 180.881000 206.856000 40.923900 87.340800 21.084700 118.524000 110.803000 16.687293 27.209084
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:LDHC 20 0.902540 277.956000 247.240000 262.759000 260.445000 308.856000 381.352000 321.682000 316.355000 242.073000 257.565000 306.698000 368.740000 14.313803 26.092460
ATTED:At1g01010.html 261585_at Diurnal_Condition:LDHC 21 0.957951 13.175600 10.580300 8.676940 8.116520 8.006380 18.697700 13.403400 7.916100 8.646590 7.502840 10.282000 17.397800 15.455113 2.167712
ATTED:At1g01040.html 261584_at Diurnal_Condition:LDHC 22 0.811560 54.112100 47.166500 50.969900 49.177200 53.018200 70.249100 90.322400 50.120200 38.353500 50.045400 51.562100 86.317800 20.709830 8.257949
ATTED:At2g26570.html 245028_at Diurnal_Condition:LDHC 4 0.812732 194.629000 214.133000 170.395000 168.674000 66.352900 113.876000 172.648000 269.963000 277.392000 144.155000 162.210000 152.608000 23.092952 32.436169
ATTED:At2g26580.html 245029_at Diurnal_Condition:LDHC 15 0.822634 187.179000 114.062000 232.505000 280.613000 214.907000 279.582000 134.802000 159.739000 183.231000 219.482000 265.728000 282.718000 9.717811 30.848561
* Row count is limited to 100.