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MCL coexpression mm9:1447: Difference between revisions

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{{MCL_coexpression_mm9
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specification process;0.00774099031919663;15436,15437!GO:0005667;transcription factor complex;0.00774099031919663;15436,15437!GO:0043565;sequence-specific DNA binding;0.00774099031919663;15436,15437!GO:0009887;organ morphogenesis;0.00774099031919663;15436,15437!GO:0044451;nucleoplasm part;0.00774099031919663;15436,15437!GO:0005654;nucleoplasm;0.00774099031919663;15436,15437!GO:0031981;nuclear lumen;0.00927992739384473;15436,15437!GO:0031974;membrane-enclosed lumen;0.00927992739384473;15436,15437!GO:0043233;organelle lumen;0.00927992739384473;15436,15437!GO:0003700;transcription factor activity;0.0100769759894287;15436,15437!GO:0044428;nuclear part;0.0134197692955157;15436,15437!GO:0009653;anatomical structure morphogenesis;0.0159826463630404;15436,15437!GO:0048513;organ development;0.0209993850407017;15436,15437!GO:0043234;protein complex;0.0249859407258191;15436,15437!GO:0048731;system development;0.0249859407258191;15436,15437!GO:0006355;regulation of transcription, DNA-dependent;0.0249859407258191;15436,15437!GO:0006351;transcription, DNA-dependent;0.0249859407258191;15436,15437!GO:0032774;RNA biosynthetic process;0.0249859407258191;15436,15437!GO:0003677;DNA binding;0.0249859407258191;15436,15437!GO:0045449;regulation of transcription;0.0249859407258191;15436,15437!GO:0048856;anatomical structure development;0.0249859407258191;15436,15437!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0249859407258191;15436,15437!GO:0006350;transcription;0.0249859407258191;15436,15437!GO:0032991;macromolecular complex;0.0249859407258191;15436,15437!GO:0010468;regulation of gene expression;0.0249859407258191;15436,15437!GO:0031323;regulation of cellular metabolic process;0.0259960277491642;15436,15437!GO:0007275;multicellular organismal development;0.0259960277491642;15436,15437!GO:0019222;regulation of metabolic process;0.0259960277491642;15436,15437!GO:0016070;RNA metabolic process;0.0264421083823468;15436,15437!GO:0044446;intracellular organelle part;0.0265077605788722;15436,15437!GO:0044422;organelle part;0.0265077605788722;15436,15437!GO:0010467;gene expression;0.0343177985962733;15436,15437!GO:0003676;nucleic acid binding;0.0349031074208671;15436,15437!GO:0032502;developmental process;0.0360811872666491;15436,15437!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0382194453525193;15436,15437!GO:0050794;regulation of cellular 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|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.00774099031919663;15436,15437!GO:0005667;transcription factor complex;0.00774099031919663;15436,15437!GO:0043565;sequence-specific DNA binding;0.00774099031919663;15436,15437!GO:0009887;organ morphogenesis;0.00774099031919663;15436,15437!GO:0044451;nucleoplasm part;0.00774099031919663;15436,15437!GO:0005654;nucleoplasm;0.00774099031919663;15436,15437!GO:0031981;nuclear lumen;0.00927992739384473;15436,15437!GO:0031974;membrane-enclosed lumen;0.00927992739384473;15436,15437!GO:0043233;organelle lumen;0.00927992739384473;15436,15437!GO:0003700;transcription factor activity;0.0100769759894287;15436,15437!GO:0044428;nuclear part;0.0134197692955157;15436,15437!GO:0009653;anatomical structure morphogenesis;0.0159826463630404;15436,15437!GO:0048513;organ development;0.0209993850407017;15436,15437!GO:0043234;protein complex;0.0249859407258191;15436,15437!GO:0048731;system development;0.0249859407258191;15436,15437!GO:0006355;regulation of transcription, DNA-dependent;0.0249859407258191;15436,15437!GO:0006351;transcription, DNA-dependent;0.0249859407258191;15436,15437!GO:0032774;RNA biosynthetic process;0.0249859407258191;15436,15437!GO:0003677;DNA binding;0.0249859407258191;15436,15437!GO:0045449;regulation of transcription;0.0249859407258191;15436,15437!GO:0048856;anatomical structure development;0.0249859407258191;15436,15437!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0249859407258191;15436,15437!GO:0006350;transcription;0.0249859407258191;15436,15437!GO:0032991;macromolecular complex;0.0249859407258191;15436,15437!GO:0010468;regulation of gene expression;0.0249859407258191;15436,15437!GO:0031323;regulation of cellular metabolic process;0.0259960277491642;15436,15437!GO:0007275;multicellular organismal development;0.0259960277491642;15436,15437!GO:0019222;regulation of metabolic process;0.0259960277491642;15436,15437!GO:0016070;RNA metabolic process;0.0264421083823468;15436,15437!GO:0044446;intracellular organelle part;0.0265077605788722;15436,15437!GO:0044422;organelle part;0.0265077605788722;15436,15437!GO:0010467;gene expression;0.0343177985962733;15436,15437!GO:0003676;nucleic acid binding;0.0349031074208671;15436,15437!GO:0032502;developmental process;0.0360811872666491;15436,15437!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0382194453525193;15436,15437!GO:0050794;regulation of cellular process;0.0427343490279872;15436,15437!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000489!4.65e-17!21;UBERON:0005156!1.07e-13!26;UBERON:0000990!1.07e-13!26;UBERON:0006554!3.29e-13!18;UBERON:0003133!3.59e-13!24;UBERON:0001008!3.61e-13!19;UBERON:0002113!8.74e-13!14;UBERON:0003918!8.74e-13!14;UBERON:0011143!8.74e-13!14;UBERON:0005095!8.74e-13!14;UBERON:0007687!8.74e-13!14;UBERON:0000991!1.04e-10!18;UBERON:0005564!1.04e-10!18;UBERON:0004176!5.77e-10!17;UBERON:0009196!5.77e-10!17;UBERON:0009117!5.77e-10!17;UBERON:0003135!6.63e-09!15;UBERON:0003101!8.39e-09!16;UBERON:0000079!8.39e-09!16;UBERON:0003064!3.48e-08!14;UBERON:0000473!4.50e-08!14;UBERON:0003886!2.78e-07!38;UBERON:0002553!7.36e-07!39
|tfbs_overrepresentation_for_novel_motifs=0.491922,1.24447,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,1.31693,2.04718,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.442204,0.426133,0.108444,0.657163,0.345236,2.0696,0.686615,0.63639,0.572827,0.394364,0.181062,0.558142,0.960397,0.336199,0.204204,0.364821,0.951637,3.28478,0.629145,0.303703,0.27383,0.342638,0.56353,0.0995018,0.366415,0.0417367,1.30113,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,1.58094,1.10437,1.12205,0.66551,2.76451,1.50238,0.21472,0.663395,0.939962,1.72013,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.740068,1.156,0.599223,0.19692,0.204132,0.763395,0.922432,0.430551,0.254777,2.03037,0.722675,0.240896,1.03903,0.439832,0.220054,1.02367,0.780154,6.09545,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,1.38336,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,1.35637,0.53982,0.858327,0.862623,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,3.22333,0.564002,0.778321,2.10357,0.503174,0.348692,0.540361,1.10885,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.5667
}}

Latest revision as of 16:57, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:74542918..74542971,+p1@Hoxd8
Mm9::chr2:74542974..74542986,+p5@Hoxd8
Mm9::chr2:74543103..74543135,+p4@Hoxd8
Mm9::chr2:74543202..74543213,+p3@Hoxd8
Mm9::chr2:74543235..74543246,+p7@Hoxd8
Mm9::chr2:74560109..74560131,+p1@Hoxd4


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:0007389pattern specification process0.00774099031919663
GO:0005667transcription factor complex0.00774099031919663
GO:0043565sequence-specific DNA binding0.00774099031919663
GO:0009887organ morphogenesis0.00774099031919663
GO:0044451nucleoplasm part0.00774099031919663
GO:0005654nucleoplasm0.00774099031919663
GO:0031981nuclear lumen0.00927992739384473
GO:0031974membrane-enclosed lumen0.00927992739384473
GO:0043233organelle lumen0.00927992739384473
GO:0003700transcription factor activity0.0100769759894287
GO:0044428nuclear part0.0134197692955157
GO:0009653anatomical structure morphogenesis0.0159826463630404
GO:0048513organ development0.0209993850407017
GO:0043234protein complex0.0249859407258191
GO:0048731system development0.0249859407258191
GO:0006355regulation of transcription, DNA-dependent0.0249859407258191
GO:0006351transcription, DNA-dependent0.0249859407258191
GO:0032774RNA biosynthetic process0.0249859407258191
GO:0003677DNA binding0.0249859407258191
GO:0045449regulation of transcription0.0249859407258191
GO:0048856anatomical structure development0.0249859407258191
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0249859407258191
GO:0006350transcription0.0249859407258191
GO:0032991macromolecular complex0.0249859407258191
GO:0010468regulation of gene expression0.0249859407258191
GO:0031323regulation of cellular metabolic process0.0259960277491642
GO:0007275multicellular organismal development0.0259960277491642
GO:0019222regulation of metabolic process0.0259960277491642
GO:0016070RNA metabolic process0.0264421083823468
GO:0044446intracellular organelle part0.0265077605788722
GO:0044422organelle part0.0265077605788722
GO:0010467gene expression0.0343177985962733
GO:0003676nucleic acid binding0.0349031074208671
GO:0032502developmental process0.0360811872666491
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0382194453525193
GO:0050794regulation of cellular process0.0427343490279872



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>

Uber Anatomy
Ontology termp-valuen
cavitated compound organ4.65e-1721
reproductive structure1.07e-1326
reproductive system1.07e-1326
urinary system structure3.29e-1318
reproductive organ3.59e-1324
renal system3.61e-1319
kidney8.74e-1314
kidney mesenchyme8.74e-1314
upper urinary tract8.74e-1314
kidney rudiment8.74e-1314
kidney field8.74e-1314
gonad1.04e-1018
gonad primordium1.04e-1018
external genitalia5.77e-1017
indifferent external genitalia5.77e-1017
indifferent gonad5.77e-1017
male reproductive organ6.63e-0915
male organism8.39e-0916
male reproductive system8.39e-0916
intermediate mesoderm3.48e-0814
testis4.50e-0814
body cavity precursor2.78e-0738
anatomical cavity7.36e-0739


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)
MA0003.16.9092
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.304529
MA0017.10.387481
MA0019.10.800946
MA0024.15.08891
MA0025.11.22395
MA0027.12.64231
MA0028.11.72321
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.149949
MA0058.11.11298
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.753052
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.725434
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.14.99448
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.13.00715
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.12.57126
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.13.91632
MA0146.10.990842
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.21.5257
MA0039.20.181031
MA0138.20.788113
MA0002.20.689262
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.76177
MA0065.20.380324
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.11.33283
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.11.08528
MA0163.18.27119
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.25.82723
MA0102.21.7182
MA0258.10.290587
MA0259.10.833237
MA0442.10
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