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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_LL12_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
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:LL12_LDHH 23 0.635301 6.723930 6.765500 6.654860 5.132370 5.887480 9.390520 6.608190 7.565290 5.797030 5.602410 5.975580 6.067410 17.667018 0.446213
ATTED:At1g01050.html 31 HeptamerElement:ATATAAA ATATAAA 0.08 261579_at Circadian_Condition:LL12_LDHH 20 0.437990 689.501000 679.264000 674.102000 732.098000 667.431000 810.819000 651.177000 706.030000 666.541000 656.359000 693.760000 653.215000 22.879702 7.485132
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:LL12_LDHH 1 0.921307 554.284000 484.413000 52.300400 12.842500 20.930900 203.117000 485.217000 260.745000 80.974000 20.080200 90.130300 214.936000 18.777304 124.741965
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:LL12_LDHH 4 0.842840 17.847200 17.154800 13.487300 16.342000 7.982460 11.123500 11.802000 20.348400 15.978100 13.556700 8.873000 9.229270 23.194360 2.196444
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Circadian_Condition:LL12_LDHH 17 0.614213 260.319000 163.600000 173.628000 218.322000 166.995000 181.444000 159.371000 120.747000 174.413000 283.274000 212.768000 248.117000 2.007209 14.760776
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:LL12_LDHH 23 0.579996 1893.340000 1760.070000 1826.300000 1686.580000 1585.930000 1817.800000 1814.150000 1446.410000 1614.840000 1721.610000 1721.830000 1683.060000 19.772869 25.955911
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Circadian_Condition:LL12_LDHH 15 0.846622 4061.250000 3040.940000 3514.070000 4380.890000 4222.210000 3526.330000 2733.840000 3403.820000 3746.960000 4154.690000 4048.280000 3598.730000 7.884582 257.487298
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Circadian_Condition:LL12_LDHH 13 0.798804 252.859000 238.471000 360.608000 336.984000 323.445000 355.585000 215.691000 320.808000 376.535000 393.675000 290.596000 342.704000 6.170235 25.768671
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Circadian_Condition:LL12_LDHH 5 0.310028 5.409250 5.532480 5.627060 6.083010 4.376040 4.854370 5.025850 4.247630 4.310860 4.007390 5.270930 4.786710 14.347826 0.037983
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Circadian_Condition:LL12_LDHH 5 0.868889 13.096200 19.979100 14.159400 10.551000 9.844280 7.549570 10.597500 15.122400 16.053000 9.529800 9.047460 10.307800 23.158426 2.112553
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:LL12_LDHH 8 0.427181 66.990100 61.898400 51.552900 81.375700 56.802500 43.780900 46.726400 67.615200 88.958200 55.477500 78.115600 70.604100 4.349080 3.570135
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Circadian_Condition:LL12_LDHH 2 0.813604 22.914900 28.242900 16.777700 19.138500 16.479400 12.454400 22.821300 22.618500 18.534100 15.601100 17.082100 20.891800 20.786336 2.086173
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:LL12_LDHH 7 0.505176 7.334920 8.827660 12.301500 5.284520 7.716720 11.341900 7.990930 10.976100 11.772600 10.863000 11.399600 10.934300 2.173842 0.212925
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:LL12_LDHH 4 0.565979 229.925000 235.943000 213.704000 200.884000 217.084000 217.737000 181.491000 227.623000 208.547000 217.929000 208.974000 214.032000 21.758803 2.425709
ATTED:At1g01010.html 261585_at Circadian_Condition:LL12_LDHH 10 0.571267 7.786760 8.526680 12.474300 9.710990 9.913910 11.306100 8.295340 15.346400 10.366300 11.792900 7.774930 10.542300 10.370006 0.568935
ATTED:At1g01040.html 261584_at Circadian_Condition:LL12_LDHH 6 0.550054 45.609300 46.513900 43.938700 38.838800 45.045500 30.023600 53.680300 46.480400 52.311500 50.885100 34.428900 48.005300 12.980452 2.368315
ATTED:At2g26570.html 245028_at Circadian_Condition:LL12_LDHH 1 0.495856 295.779000 308.737000 212.088000 253.368000 248.640000 213.252000 246.342000 183.531000 243.855000 176.594000 196.464000 204.210000 20.165541 11.508954
ATTED:At2g26580.html 245029_at Circadian_Condition:LL12_LDHH 10 0.366428 74.431700 45.834700 83.905300 60.963000 41.177300 47.691100 51.934500 47.846200 42.405500 50.450700 90.284300 52.220300 7.993663 1.647486
* Row count is limited to 100.