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MCL coexpression mm9:1601: Difference between revisions

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{{MCL_coexpression_mm9
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specification process;0.00788985551764272;15414,15415!GO:0005667;transcription factor complex;0.00788985551764272;15414,15415!GO:0043565;sequence-specific DNA binding;0.00788985551764272;15414,15415!GO:0009887;organ morphogenesis;0.00788985551764272;15414,15415!GO:0044451;nucleoplasm part;0.00788985551764272;15414,15415!GO:0005654;nucleoplasm;0.00788985551764272;15414,15415!GO:0031981;nuclear lumen;0.00945838753603405;15414,15415!GO:0031974;membrane-enclosed lumen;0.00945838753603405;15414,15415!GO:0043233;organelle lumen;0.00945838753603405;15414,15415!GO:0003700;transcription factor activity;0.0102707639892254;15414,15415!GO:0044428;nuclear part;0.0136778417819679;15414,15415!GO:0009653;anatomical structure morphogenesis;0.0162900049469451;15414,15415!GO:0048513;organ development;0.0214032193684075;15414,15415!GO:0043234;protein complex;0.025466439585931;15414,15415!GO:0048731;system development;0.025466439585931;15414,15415!GO:0006355;regulation of transcription, DNA-dependent;0.025466439585931;15414,15415!GO:0006351;transcription, DNA-dependent;0.025466439585931;15414,15415!GO:0032774;RNA biosynthetic process;0.025466439585931;15414,15415!GO:0003677;DNA binding;0.025466439585931;15414,15415!GO:0045449;regulation of transcription;0.025466439585931;15414,15415!GO:0048856;anatomical structure development;0.025466439585931;15414,15415!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.025466439585931;15414,15415!GO:0006350;transcription;0.025466439585931;15414,15415!GO:0032991;macromolecular complex;0.025466439585931;15414,15415!GO:0010468;regulation of gene expression;0.025466439585931;15414,15415!GO:0031323;regulation of cellular metabolic process;0.0264959513597251;15414,15415!GO:0007275;multicellular organismal development;0.0264959513597251;15414,15415!GO:0019222;regulation of metabolic process;0.0264959513597251;15414,15415!GO:0016070;RNA metabolic process;0.0269506104666227;15414,15415!GO:0044446;intracellular organelle part;0.0270175252053889;15414,15415!GO:0044422;organelle part;0.0270175252053889;15414,15415!GO:0010467;gene expression;0.0349777562615863;15414,15415!GO:0003676;nucleic acid binding;0.0355743210251145;15414,15415!GO:0032502;developmental process;0.0367750562525462;15414,15415!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0389544346862216;15414,15415!GO:0050794;regulation of cellular 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|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.00788985551764272;15414,15415!GO:0005667;transcription factor complex;0.00788985551764272;15414,15415!GO:0043565;sequence-specific DNA binding;0.00788985551764272;15414,15415!GO:0009887;organ morphogenesis;0.00788985551764272;15414,15415!GO:0044451;nucleoplasm part;0.00788985551764272;15414,15415!GO:0005654;nucleoplasm;0.00788985551764272;15414,15415!GO:0031981;nuclear lumen;0.00945838753603405;15414,15415!GO:0031974;membrane-enclosed lumen;0.00945838753603405;15414,15415!GO:0043233;organelle lumen;0.00945838753603405;15414,15415!GO:0003700;transcription factor activity;0.0102707639892254;15414,15415!GO:0044428;nuclear part;0.0136778417819679;15414,15415!GO:0009653;anatomical structure morphogenesis;0.0162900049469451;15414,15415!GO:0048513;organ development;0.0214032193684075;15414,15415!GO:0043234;protein complex;0.025466439585931;15414,15415!GO:0048731;system development;0.025466439585931;15414,15415!GO:0006355;regulation of transcription, DNA-dependent;0.025466439585931;15414,15415!GO:0006351;transcription, DNA-dependent;0.025466439585931;15414,15415!GO:0032774;RNA biosynthetic process;0.025466439585931;15414,15415!GO:0003677;DNA binding;0.025466439585931;15414,15415!GO:0045449;regulation of transcription;0.025466439585931;15414,15415!GO:0048856;anatomical structure development;0.025466439585931;15414,15415!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.025466439585931;15414,15415!GO:0006350;transcription;0.025466439585931;15414,15415!GO:0032991;macromolecular complex;0.025466439585931;15414,15415!GO:0010468;regulation of gene expression;0.025466439585931;15414,15415!GO:0031323;regulation of cellular metabolic process;0.0264959513597251;15414,15415!GO:0007275;multicellular organismal development;0.0264959513597251;15414,15415!GO:0019222;regulation of metabolic process;0.0264959513597251;15414,15415!GO:0016070;RNA metabolic process;0.0269506104666227;15414,15415!GO:0044446;intracellular organelle part;0.0270175252053889;15414,15415!GO:0044422;organelle part;0.0270175252053889;15414,15415!GO:0010467;gene expression;0.0349777562615863;15414,15415!GO:0003676;nucleic acid binding;0.0355743210251145;15414,15415!GO:0032502;developmental process;0.0367750562525462;15414,15415!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0389544346862216;15414,15415!GO:0050794;regulation of cellular process;0.0435561634323716;15414,15415!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000489!4.54e-18!21;UBERON:0002113!9.84e-13!14;UBERON:0003918!9.84e-13!14;UBERON:0011143!9.84e-13!14;UBERON:0005095!9.84e-13!14;UBERON:0007687!9.84e-13!14;UBERON:0001008!4.25e-12!19;UBERON:0006554!1.54e-11!18;UBERON:0003064!1.86e-10!14
|tfbs_overrepresentation_for_novel_motifs=0.557864,1.02681,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.836099,0.370407,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.775038,0.185796,0.489529,0.145201,0.727684,0.404661,0.537749,0.757752,0.754069,0.641282,0.456327,0.227599,0.626183,1.03545,0.395107,0.704734,0.425309,0.791367,0.384813,0.699032,0.360612,0.876199,0.401916,0.631725,0.134724,0.426986,0.0637209,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.731291,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,0.257421,0.686172,0.70455,0.835925,0.997094,1.23692,0.308173,0.948899,0.794502,1.44895,1.1148,0.574099,2.10516,1.87702,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.937248,0.3366,0.806207,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,1.35621,1.16464,0.495367,1.61686,1.41481,1.03353,0.673306,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,1.06895,1.14546,0.595426,1.3055,0.750642,1.43666,0.44142,0.566955,1.53084,1.3869,2.2222,1.82084,1.34183,0.772375,2.38006,0.905521,0.632211,0.851091,2.18247,0.569503,1.05179,0.651755,0.133815,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.745913
}}

Latest revision as of 17:11, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:96145393..96145407,+p3@Hoxb7
Mm9::chr11:96146882..96146905,+p@chr11:96146882..96146905
+
Mm9::chr11:96146907..96146941,+p@chr11:96146907..96146941
+
Mm9::chr11:96147952..96147967,+p1@Hoxb7
Mm9::chr11:96160068..96160084,+p6@Hoxb6


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 process0.00788985551764272
GO:0005667transcription factor complex0.00788985551764272
GO:0043565sequence-specific DNA binding0.00788985551764272
GO:0009887organ morphogenesis0.00788985551764272
GO:0044451nucleoplasm part0.00788985551764272
GO:0005654nucleoplasm0.00788985551764272
GO:0031981nuclear lumen0.00945838753603405
GO:0031974membrane-enclosed lumen0.00945838753603405
GO:0043233organelle lumen0.00945838753603405
GO:0003700transcription factor activity0.0102707639892254
GO:0044428nuclear part0.0136778417819679
GO:0009653anatomical structure morphogenesis0.0162900049469451
GO:0048513organ development0.0214032193684075
GO:0043234protein complex0.025466439585931
GO:0048731system development0.025466439585931
GO:0006355regulation of transcription, DNA-dependent0.025466439585931
GO:0006351transcription, DNA-dependent0.025466439585931
GO:0032774RNA biosynthetic process0.025466439585931
GO:0003677DNA binding0.025466439585931
GO:0045449regulation of transcription0.025466439585931
GO:0048856anatomical structure development0.025466439585931
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.025466439585931
GO:0006350transcription0.025466439585931
GO:0032991macromolecular complex0.025466439585931
GO:0010468regulation of gene expression0.025466439585931
GO:0031323regulation of cellular metabolic process0.0264959513597251
GO:0007275multicellular organismal development0.0264959513597251
GO:0019222regulation of metabolic process0.0264959513597251
GO:0016070RNA metabolic process0.0269506104666227
GO:0044446intracellular organelle part0.0270175252053889
GO:0044422organelle part0.0270175252053889
GO:0010467gene expression0.0349777562615863
GO:0003676nucleic acid binding0.0355743210251145
GO:0032502developmental process0.0367750562525462
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0389544346862216
GO:0050794regulation of cellular process0.0435561634323716



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 organ4.54e-1821
kidney9.84e-1314
kidney mesenchyme9.84e-1314
upper urinary tract9.84e-1314
kidney rudiment9.84e-1314
kidney field9.84e-1314
renal system4.25e-1219
urinary system structure1.54e-1118
intermediate mesoderm1.86e-1014


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
MA0004.11.46913
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.187732
MA0017.10.449113
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
MA0042.11.26591
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.602741
MA0056.10
MA0057.11.68574
MA0058.13.19314
MA0059.12.20622
MA0060.10.881183
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.14.96534
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.121.1554
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
MA0093.11.96218
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.693075
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
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
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.11.48363
MA0146.10.0604336
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.22.26967
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.845917
MA0047.20.75686
MA0112.20.157681
MA0065.21.48609
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.99229
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.11.35147
MA0163.15.11865
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.215.2775
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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