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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_LLHC
#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_LLHC 4 0.662349 10.803800 9.217910 11.056000 8.090380 7.741600 7.798260 10.303100 8.374890 6.943640 7.335630 7.811570 8.866190 16.276840 0.558647
ATTED:At1g01050.html 31 HeptamerElement:ATATAAA ATATAAA 0.08 261579_at Circadian_Condition:LL_LLHC 21 0.792242 967.443000 690.732000 376.224000 612.186000 914.743000 714.140000 770.781000 678.014000 547.865000 662.967000 744.838000 725.833000 14.632297 75.434245
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_LLHC 2 0.951721 1358.800000 967.657000 41.369000 5.162730 5.907350 108.381000 1045.930000 1015.070000 104.384000 7.267420 11.185000 481.797000 19.340909 319.247595
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_LLHC 8 0.626994 13.701500 14.237100 18.410800 15.275000 15.022700 8.237440 14.655600 14.567500 11.366300 8.758260 10.828100 11.930300 12.348721 0.910460
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Circadian_Condition:LL_LLHC 16 0.607727 572.950000 394.806000 579.101000 472.801000 494.375000 543.235000 448.864000 354.644000 403.199000 420.866000 485.294000 439.142000 12.250074 16.655864
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_LLHC 8 0.603580 2518.360000 2106.380000 3281.660000 2668.380000 2431.210000 2310.600000 2318.040000 2544.510000 2440.740000 2293.270000 2579.000000 2314.100000 3.544482 88.890144
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Circadian_Condition:LL_LLHC 19 0.607574 6402.550000 6486.280000 5337.110000 6033.000000 6848.410000 6818.170000 7150.560000 6338.590000 6754.170000 7149.220000 6872.500000 6997.400000 13.272144 200.101459
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Circadian_Condition:LL_LLHC 15 0.906729 305.170000 204.155000 338.655000 364.797000 427.481000 332.243000 287.267000 240.868000 353.184000 425.463000 333.008000 293.803000 7.940100 37.047998
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Circadian_Condition:LL_LLHC 19 0.689047 5.966800 5.109280 4.728030 5.550160 6.198350 5.266920 5.482570 5.269760 5.587810 5.247180 6.007700 5.807840 12.201052 0.186882
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Circadian_Condition:LL_LLHC 8 0.840460 9.841690 35.302800 137.702000 62.522300 29.854200 19.934800 24.745300 40.100200 61.578900 68.319600 18.881700 15.070700 2.996509 19.470200
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_LLHC 11 0.403484 121.864000 172.917000 230.878000 195.863000 233.665000 162.557000 171.652000 156.799000 130.524000 138.907000 131.483000 109.462000 7.617489 9.475385
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Circadian_Condition:LL_LLHC 8 0.676573 60.671400 33.027000 85.885300 42.856000 49.144600 49.716200 37.140500 41.271600 52.279800 38.041700 52.485900 39.534700 3.240740 2.355788
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_LLHC 10 0.674604 8.276050 12.388800 11.366300 21.665400 13.055700 11.737800 10.593200 11.648100 73.771300 43.719600 10.193700 7.855670 8.403958 8.132662
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_LLHC 18 0.557229 335.281000 329.953000 240.950000 267.353000 334.131000 261.531000 249.044000 197.794000 276.096000 310.459000 250.046000 295.879000 11.930745 6.986654
ATTED:At1g01010.html 261585_at Circadian_Condition:LL_LLHC 18 0.482422 11.896900 9.553900 8.933160 10.217200 13.811400 11.107500 7.918760 6.363980 7.084290 7.276060 7.525010 8.366780 12.660038 0.650207
ATTED:At1g01040.html 261584_at Circadian_Condition:LL_LLHC 23 0.557457 73.119900 57.326200 61.699000 58.785700 58.096800 80.986100 65.039800 74.826300 60.917900 64.701900 66.261100 56.783100 17.086893 2.242567
ATTED:At2g26570.html 245028_at Circadian_Condition:LL_LLHC 9 0.559943 234.026000 199.978000 397.111000 270.547000 234.885000 213.132000 214.849000 218.386000 202.841000 181.083000 116.084000 193.459000 10.917959 19.599595
ATTED:At2g26580.html 245029_at Circadian_Condition:LL_LLHC 18 0.423175 159.009000 98.733200 51.461500 129.197000 137.138000 161.964000 141.740000 198.338000 190.347000 218.301000 204.426000 223.395000 12.065196 13.572833
* Row count is limited to 100.