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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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#lang en
#attribution_name GenoCon_2
#attribution_url http://atted.jp/download.shtml
#license http://creativecommons.org/publicdomain/zero/1.0/deed.ja
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#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
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#property_context Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion Assertion
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ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:LIGHT5_znknOX 10 0.951561 164.000000 167.000000 249.000000 249.000000 130.000000 162.000000 180.376000 171.696000 269.874000 248.014000 134.878000 163.804000 2.837558 26.150992
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:LIGHT5_znknOX 22 0.893947 3852.000000 3396.000000 3126.000000 2972.000000 3116.000000 4370.000000 3855.420000 3312.330000 3437.600000 2790.600000 3149.040000 4059.880000 16.554543 277.966657
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:LIGHT5_znknOX 19 0.695422 9586.000000 8678.000000 8140.000000 9148.000000 9436.000000 8447.000000 9913.670000 8249.370000 7629.780000 8432.270000 10303.900000 8888.870000 13.258097 333.950651
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ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:LIGHT5_znknOX 10 0.794808 8.000000 6.000000 13.000000 12.000000 6.000000 11.000000 8.587270 5.602770 13.635700 11.159900 6.163380 10.345200 4.444754 0.861984
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:LIGHT5_znknOX 10 0.924752 17.000000 33.000000 53.000000 64.000000 13.000000 20.000000 16.782600 34.464400 52.881400 66.806800 12.147100 20.771700 3.291161 11.905415
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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:LIGHT5_znknOX 8 0.958152 10.000000 10.000000 30.000000 12.000000 13.000000 15.000000 10.273100 9.105210 28.871700 12.772800 12.817000 15.696400 3.315489 2.396493
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:LIGHT5_znknOX 20 0.915670 309.000000 277.000000 247.000000 256.000000 327.000000 349.000000 285.340000 292.805000 244.490000 246.382000 320.090000 337.251000 14.173613 23.305944
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ATTED:At2g26570.html 245028_at Diurnal_Condition:LIGHT5_znknOX 3 0.848008 81.000000 58.000000 70.000000 53.000000 34.000000 63.000000 84.195600 58.305800 72.281600 50.172000 34.046700 60.188500 20.485724 8.023754
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* Row count is limited to 100.