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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_lhyox_SD
#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:lhyox_SD 11 0.952797 4.759360 5.529820 6.136340 6.181150 5.816710 4.784930 5.045570 5.005970 6.441270 6.396430 6.214930 5.189720 5.250290 0.409704
ATTED:At1g01050.html 31 HeptamerElement:ATATAAA ATATAAA 0.08 261579_at Diurnal_Condition:lhyox_SD 20 0.930287 3797.190000 2045.890000 2314.090000 2471.970000 4394.640000 3405.240000 3670.040000 2131.910000 2418.440000 2251.310000 4176.180000 3280.850000 13.033308 475.310972
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:lhyox_SD 17 0.853081 8039.950000 5544.810000 6728.040000 6878.300000 7813.810000 7247.500000 7596.350000 5305.120000 7045.610000 6386.830000 7365.160000 7951.690000 12.696859 422.309510
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:lhyox_SD 16 0.918426 37.429300 13.631100 22.609000 16.954600 73.649100 31.373700 35.064000 13.454400 23.335600 16.520900 71.213800 30.094500 11.600797 9.672950
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:lhyox_SD 10 0.935968 102.108000 196.946000 291.851000 298.988000 156.064000 156.717000 102.774000 179.573000 306.870000 327.568000 163.827000 168.261000 4.109931 50.208191
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:lhyox_SD 22 0.960418 3247.210000 3235.970000 2371.680000 2549.660000 3231.300000 3400.900000 3490.670000 3052.610000 2265.810000 2385.260000 3235.400000 3428.800000 15.590074 289.994927
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:lhyox_SD 13 0.887122 4678.400000 4789.130000 4863.060000 5355.980000 4674.160000 4373.390000 4512.230000 4608.630000 4580.670000 5732.570000 5098.530000 4770.200000 6.110642 186.366094
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Diurnal_Condition:lhyox_SD 19 0.974101 161.311000 69.007600 37.314200 113.834000 225.277000 188.523000 153.184000 73.418600 37.138900 118.164000 221.040000 207.346000 12.637712 45.763937
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Diurnal_Condition:lhyox_SD 4 0.894331 3.527880 4.080490 3.586950 3.392300 3.319400 3.108440 3.221520 4.053080 3.296300 3.362690 3.534500 3.404750 22.836386 0.124805
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:lhyox_SD 0 0.999463 70.199800 7.199090 7.251170 7.988620 5.435230 7.234090 70.883000 7.023330 7.499880 8.240180 5.800940 6.565690 18.103455 10.493139
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:lhyox_SD 10 0.928106 20.517700 32.658600 68.911800 52.414500 16.127100 23.174600 18.929700 34.326500 64.205200 52.014600 15.972900 24.513600 2.726606 11.487396
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Diurnal_Condition:lhyox_SD 8 0.931077 11.767300 36.211800 30.916600 43.339700 16.648800 11.989400 12.182300 39.700800 29.145800 45.575200 18.083400 12.304600 2.870246 7.599826
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:lhyox_SD 23 0.948792 464.446000 8.948680 7.654230 80.925500 161.563000 203.934000 503.542000 8.132160 8.070460 77.133900 155.858000 190.156000 15.686845 86.046739
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:lhyox_SD 4 0.941083 274.509000 343.266000 265.830000 266.568000 243.584000 272.627000 250.964000 347.249000 277.985000 284.133000 262.826000 266.582000 22.563728 14.642002
ATTED:At1g01010.html 261585_at Diurnal_Condition:lhyox_SD 22 0.971081 15.068200 7.405670 9.165320 6.632570 8.690430 15.527300 15.630300 7.452860 8.890260 6.081050 8.479310 16.430400 15.962678 2.301356
ATTED:At1g01040.html 261584_at Diurnal_Condition:lhyox_SD 23 0.919908 59.952900 44.979000 44.982100 42.861300 45.934600 49.475200 57.799400 47.409000 42.001100 39.963800 46.965700 53.433300 19.230943 3.745626
ATTED:At2g26570.html 245028_at Diurnal_Condition:lhyox_SD 0 0.937797 319.053000 198.075000 176.207000 130.121000 173.856000 236.553000 329.091000 195.105000 191.250000 124.976000 191.038000 241.077000 17.418563 38.973698
ATTED:At2g26580.html 245029_at Diurnal_Condition:lhyox_SD 4 0.826579 27.831100 75.679800 36.503300 62.481000 37.022300 32.178600 29.080500 81.789400 38.082200 56.831400 37.804900 31.743600 1.206683 7.084301
* Row count is limited to 100.