Contact

Link and Publish your data

to the Linked Open Data Community

Linkdata Work Information

GenoCon2 Challenge A - Circadian Coexpression (DIURNAL + ATTED-II promoter motif)

Open Smart Phone View
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

value

useful
0
Loading...



Select a file name to see the detais.
Show API List
   
#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_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 Diurnal_Condition:LLHC 4 0.821260 8.410920 11.597300 8.390690 9.434340 9.058090 9.172810 7.964010 9.813660 8.145820 8.292160 8.389410 8.409150 22.365124 0.231469
ATTED:At1g01050.html 31 HeptamerElement:ATATAAA ATATAAA 0.08 261579_at Diurnal_Condition:LLHC 21 0.889209 1124.190000 656.363000 574.253000 689.476000 890.041000 902.893000 945.225000 632.514000 602.664000 694.204000 738.901000 951.039000 14.941428 102.249474
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:LLHC 2 0.958523 1366.700000 1009.730000 98.022400 4.830500 11.272700 355.415000 1396.880000 1093.370000 70.065400 5.890910 15.196300 374.456000 19.190492 356.514686
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:LLHC 4 0.801591 9.914390 17.895400 14.274300 7.674870 5.713180 12.362500 14.556900 30.718300 23.758200 8.380860 6.859370 11.238700 22.417586 3.979137
ATTED:At1g01080.html 95 | 96 HeptamerElement:ATGGGCC | HeptamerElement:AATGGGC ATGGGCC | AATGGGC 0.08 | 0.09 261577_at Diurnal_Condition:LLHC 18 0.747823 397.981000 431.589000 465.864000 498.369000 561.666000 571.178000 483.276000 412.963000 419.786000 470.728000 432.131000 462.555000 1.263468 22.687678
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:LLHC 10 0.727425 2157.430000 2257.580000 2630.030000 2537.200000 2296.220000 2465.730000 2308.530000 2565.820000 2462.460000 2305.910000 2320.900000 2113.670000 9.305434 68.191342
ATTED:At2g26500.html 40 | 41 HeptamerElement:GATATTT | HeptamerElement:AGATATT GATATTT | AGATATT 0.10 | 0.10 245044_at Diurnal_Condition:LLHC 8 0.703231 6481.500000 6321.110000 6814.420000 7242.150000 6941.390000 5943.320000 6213.460000 6279.850000 6123.160000 6536.060000 6575.270000 5665.530000 5.385845 186.190263
ATTED:At2g26510.html 61 HeptamerElement:ATAAATA ATAAATA 0.07 245046_at Diurnal_Condition:LLHC 16 0.874062 342.208000 218.201000 317.777000 341.494000 430.472000 365.065000 267.764000 231.718000 374.268000 404.033000 324.092000 319.633000 8.763174 32.413513
ATTED:At2g26520.html 60 HeptamerElement:AAATATC AAATATC 0.12 245040_at Diurnal_Condition:LLHC 16 0.611214 5.576440 5.583430 6.649530 5.941300 6.379860 6.307290 5.997400 6.212720 5.636010 5.503280 6.890290 5.528600 2.878879 0.101384
ATTED:At2g26530.html 40 | 182 HeptamerElement:AATGGGC | HeptamerElement:AAATATC AATGGGC | AAATATC 0.07 | 0.07 245041_at Diurnal_Condition:LLHC 8 0.886740 15.427800 51.626100 79.783800 33.420000 26.463000 9.773480 12.946900 22.317700 48.528500 45.033000 28.672600 8.254110 2.706554 12.269980
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:LLHC 9 0.940886 104.597000 152.502000 223.733000 160.543000 137.689000 94.011500 115.475000 166.502000 212.798000 217.858000 134.377000 114.617000 3.084664 28.693787
ATTED:At2g26550.html 120 HeptamerElement:AATAATT AATAATT 0.07 245027_at Diurnal_Condition:LLHC 18 0.756455 43.524300 47.730500 53.987000 39.239500 56.096900 65.830600 55.393000 43.327300 34.018700 40.274300 59.956000 56.228900 13.671994 4.705095
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:LLHC 8 0.655322 20.913500 27.807600 32.895000 17.800400 28.674800 9.414970 9.315240 9.651950 15.563900 35.217700 13.115000 10.624500 4.130455 3.697833
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:LLHC 20 0.903045 327.057000 288.557000 264.401000 293.521000 326.586000 379.675000 339.302000 315.395000 276.307000 297.624000 311.497000 429.903000 14.418361 27.124406
ATTED:At1g01010.html 261585_at Diurnal_Condition:LLHC 22 0.773105 12.028000 7.907140 8.800590 9.045270 9.665930 12.037700 9.994050 9.726060 7.281770 8.399250 7.534090 9.673870 15.959960 0.736648
ATTED:At1g01040.html 261584_at Diurnal_Condition:LLHC 19 0.817518 59.876100 60.126000 54.374200 41.442200 87.102000 96.049500 60.345000 49.050900 49.136400 47.293800 52.920700 81.303900 14.020139 8.750809
ATTED:At2g26570.html 245028_at Diurnal_Condition:LLHC 7 0.593210 178.898000 222.514000 208.014000 187.259000 155.988000 224.290000 147.151000 179.267000 233.046000 190.574000 183.949000 170.240000 1.678746 8.642549
ATTED:At2g26580.html 245029_at Diurnal_Condition:LLHC 16 0.938934 155.631000 105.836000 172.589000 128.448000 328.034000 144.819000 144.963000 82.766000 126.250000 161.224000 371.097000 187.434000 10.280578 43.598819
* Row count is limited to 100.