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MCL coexpression mm9:1590: Difference between revisions

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{{MCL_coexpression_mm9
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.24837215409455,0,0.230907198759394,0.155257708002722,0,0.767238385111766,0.925300266348572|gostat_on_MCL_coexpression=GO:0042744;hydrogen peroxide catabolic process;8.27720250147647e-05;17523,13861!GO:0042743;hydrogen peroxide metabolic process;8.27720250147647e-05;17523,13861!GO:0042542;response to hydrogen peroxide;8.27720250147647e-05;17523,13861!GO:0000302;response to reactive oxygen species;0.000165435203631644;17523,13861!GO:0006800;oxygen and reactive oxygen species metabolic process;0.000415176701135355;17523,13861!GO:0004601;peroxidase activity;0.000415176701135355;17523,13861!GO:0016684;oxidoreductase activity, acting on peroxide as acceptor;0.000415176701135355;17523,13861!GO:0006118;electron transport;0.000565232096750131;17523,71361,13861!GO:0006979;response to oxidative stress;0.000604669521067218;17523,13861!GO:0006091;generation of precursor metabolites and energy;0.00099363694796803;17523,71361,13861!GO:0020037;heme binding;0.00277640050018335;17523,13861!GO:0046906;tetrapyrrole binding;0.00277640050018335;17523,13861!GO:0005615;extracellular space;0.0043754190341142;17523,328780,13861,19074!GO:0016491;oxidoreductase activity;0.00438512396045173;17523,71361,13861!GO:0044421;extracellular region part;0.00475924687139041;17523,328780,13861,19074!GO:0005506;iron ion binding;0.0143974356699051;17523,13861!GO:0044248;cellular catabolic process;0.0257939663370462;17523,13861!GO:0042221;response to chemical stimulus;0.0261439238351702;17523,13861!GO:0009056;catabolic 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|gostat_on_MCL_coexpression=GO:0042744;hydrogen peroxide catabolic process;8.27720250147647e-05;17523,13861!GO:0042743;hydrogen peroxide metabolic process;8.27720250147647e-05;17523,13861!GO:0042542;response to hydrogen peroxide;8.27720250147647e-05;17523,13861!GO:0000302;response to reactive oxygen species;0.000165435203631644;17523,13861!GO:0006800;oxygen and reactive oxygen species metabolic process;0.000415176701135355;17523,13861!GO:0004601;peroxidase activity;0.000415176701135355;17523,13861!GO:0016684;oxidoreductase activity, acting on peroxide as acceptor;0.000415176701135355;17523,13861!GO:0006118;electron transport;0.000565232096750131;17523,71361,13861!GO:0006979;response to oxidative stress;0.000604669521067218;17523,13861!GO:0006091;generation of precursor metabolites and energy;0.00099363694796803;17523,71361,13861!GO:0020037;heme binding;0.00277640050018335;17523,13861!GO:0046906;tetrapyrrole binding;0.00277640050018335;17523,13861!GO:0005615;extracellular space;0.0043754190341142;17523,328780,13861,19074!GO:0016491;oxidoreductase activity;0.00438512396045173;17523,71361,13861!GO:0044421;extracellular region part;0.00475924687139041;17523,328780,13861,19074!GO:0005506;iron ion binding;0.0143974356699051;17523,13861!GO:0044248;cellular catabolic process;0.0257939663370462;17523,13861!GO:0042221;response to chemical stimulus;0.0261439238351702;17523,13861!GO:0009056;catabolic process;0.0378805281744467;17523,13861!
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|ontology_enrichment_uberon=UBERON:0005172!5.59e-07!49;UBERON:0005173!5.59e-07!49;UBERON:0002417!5.59e-07!49;UBERON:0000916!5.59e-07!49;UBERON:0002390!6.36e-07!45;UBERON:0003061!6.36e-07!45;UBERON:0002106!8.04e-07!6;UBERON:0004457!8.04e-07!6;UBERON:0000042!8.04e-07!6;UBERON:0004854!8.04e-07!6;UBERON:0009034!8.04e-07!6;UBERON:0002095!8.04e-07!6;UBERON:0004782!8.04e-07!6;UBERON:0003281!8.04e-07!6;UBERON:0009664!8.04e-07!6;UBERON:0002296!8.04e-07!6;UBERON:0005602!8.04e-07!6;UBERON:0001179!8.04e-07!6;UBERON:0006293!8.04e-07!6
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.612204,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.370407,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.185796,0.489529,0.44579,0.727684,0.404661,0.537749,0.757752,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.253145,0.425309,0.0566307,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,0.426986,0.4934,0.591277,0.847828,0.658142,0.370501,1.16276,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.731291,0.734051,1.01481,0.796017,0.865544,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,0.257421,0.686172,0.70455,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.796301,1.1148,0.272382,0.0882907,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,1.61686,1.41481,1.82437,0.0998646,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.44142,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,0.133815,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,1.36673,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.191104
|tfbs_overrepresentation_jaspar=MA0003.1;0.406907,MA0004.1;0.603793,MA0006.1;0.419915,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.0502051,MA0017.1;1.14026,MA0019.1;0.874061,MA0024.1;1.01759,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;0.43138,MA0029.1;0.995171,MA0030.1;1.00195,MA0031.1;0.965177,MA0038.1;0.757669,MA0040.1;1.07552,MA0041.1;0.522007,MA0042.1;0.507715,MA0043.1;1.1618,MA0046.1;1.09955,MA0048.1;0.205696,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.0851423,MA0056.1;0,MA0057.1;0.562607,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;0.330907,MA0061.1;0.955135,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;0.197245,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;0.0176764,MA0074.1;0.708108,MA0076.1;0.470037,MA0077.1;1.04318,MA0078.1;0.801834,MA0081.1;0.53877,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;0.148348,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,MA0092.1;0.567278,MA0093.1;0.440484,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;0.460936,MA0105.1;1.28296,MA0106.1;0.809991,MA0107.1;0.454197,MA0108.2;2.07761,MA0109.1;0,MA0111.1;0.582193,MA0113.1;0.780358,MA0114.1;0.361633,MA0115.1;1.16466,MA0116.1;0.419688,MA0117.1;1.13165,MA0119.1;0.524046,MA0122.1;1.15196,MA0124.1;1.35963,MA0125.1;1.28445,MA0130.1;0,MA0131.1;0.869325,MA0132.1;0,MA0133.1;0,MA0135.1;1.19898,MA0136.1;0.729175,MA0139.1;0.295945,MA0140.1;1.6611,MA0141.1;1.21195,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.157686,MA0146.1;0.0604336,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;0.140205,MA0138.2;0.861035,MA0002.2;0.809945,MA0137.2;0.479301,MA0104.2;0.315156,MA0047.2;0.75686,MA0112.2;0.47695,MA0065.2;0.158101,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.587595,MA0155.1;0.515751,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.245828,MA0163.1;0.230013,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;0.0381166,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0
}}

Latest revision as of 17:10, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:87607561..87607573,+p9@Mpo
Mm9::chr11:87689026..87689036,-p1@Epx
Mm9::chr17:25435334..25435348,+p1@Prss34
Mm9::chr2:84820615..84820619,+p1@Prg2
Mm9::chr2:84828351..84828354,+p1@Prg3


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0042744hydrogen peroxide catabolic process8.27720250147647e-05
GO:0042743hydrogen peroxide metabolic process8.27720250147647e-05
GO:0042542response to hydrogen peroxide8.27720250147647e-05
GO:0000302response to reactive oxygen species0.000165435203631644
GO:0006800oxygen and reactive oxygen species metabolic process0.000415176701135355
GO:0004601peroxidase activity0.000415176701135355
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.000415176701135355
GO:0006118electron transport0.000565232096750131
GO:0006979response to oxidative stress0.000604669521067218
GO:0006091generation of precursor metabolites and energy0.00099363694796803
GO:0020037heme binding0.00277640050018335
GO:0046906tetrapyrrole binding0.00277640050018335
GO:0005615extracellular space0.0043754190341142
GO:0016491oxidoreductase activity0.00438512396045173
GO:0044421extracellular region part0.00475924687139041
GO:0005506iron ion binding0.0143974356699051
GO:0044248cellular catabolic process0.0257939663370462
GO:0042221response to chemical stimulus0.0261439238351702
GO:0009056catabolic process0.0378805281744467



Relative expression of the co-expression cluster over median <br>Analyst:




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)
MA0003.10.406907
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.0502051
MA0017.11.14026
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.10.562607
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.955135
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.0176764
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.11.28296
MA0106.10.809991
MA0107.10.454197
MA0108.22.07761
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.295945
MA0140.11.6611
MA0141.11.21195
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.157686
MA0146.10.0604336
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.140205
MA0138.20.861035
MA0002.20.809945
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.47695
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.587595
MA0155.10.515751
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.245828
MA0163.10.230013
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.0381166
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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