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MCL coexpression mm9:211: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002107!3.44e-29!22;UBERON:0007499!3.44e-29!22;UBERON:0006925!3.44e-29!22;UBERON:0009497!3.44e-29!22;UBERON:0000015!3.44e-29!22;UBERON:0002423!3.44e-29!22;UBERON:0006235!3.44e-29!22;UBERON:0008835!3.44e-29!22;UBERON:0003894!3.44e-29!22;UBERON:0004161!3.44e-29!22;UBERON:0008836!3.44e-29!22;UBERON:0009854!1.00e-27!23;UBERON:0009856!1.00e-27!23;UBERON:0002365!3.76e-25!25;UBERON:0002330!3.76e-25!25;UBERON:0005172!8.79e-17!49;UBERON:0005173!8.79e-17!49;UBERON:0002417!8.79e-17!49;UBERON:0000916!8.79e-17!49;UBERON:0003104!1.90e-12!61;UBERON:0009142!1.90e-12!61;UBERON:0005256!4.96e-12!45;UBERON:0003914!2.44e-11!47;UBERON:0009569!4.11e-11!66;UBERON:0003929!4.42e-09!55;UBERON:0005177!1.89e-08!79;UBERON:0002368!5.53e-08!60;UBERON:0004921!5.83e-08!114;UBERON:0001007!1.02e-07!116;UBERON:0001555!1.02e-07!116;UBERON:0007026!1.02e-07!116;UBERON:0004119!1.74e-07!118;UBERON:0000925!1.74e-07!118;UBERON:0006595!1.74e-07!118;UBERON:0002530!4.63e-07!65;UBERON:0000490!6.80e-07!66;UBERON:0002100!8.12e-07!90
|ontology_enrichment_uberon=UBERON:0002107!3.44e-29!22;UBERON:0007499!3.44e-29!22;UBERON:0006925!3.44e-29!22;UBERON:0009497!3.44e-29!22;UBERON:0000015!3.44e-29!22;UBERON:0002423!3.44e-29!22;UBERON:0006235!3.44e-29!22;UBERON:0008835!3.44e-29!22;UBERON:0003894!3.44e-29!22;UBERON:0004161!3.44e-29!22;UBERON:0008836!3.44e-29!22;UBERON:0009854!1.00e-27!23;UBERON:0009856!1.00e-27!23;UBERON:0002365!3.76e-25!25;UBERON:0002330!3.76e-25!25;UBERON:0005172!8.79e-17!49;UBERON:0005173!8.79e-17!49;UBERON:0002417!8.79e-17!49;UBERON:0000916!8.79e-17!49;UBERON:0003104!1.90e-12!61;UBERON:0009142!1.90e-12!61;UBERON:0005256!4.96e-12!45;UBERON:0003914!2.44e-11!47;UBERON:0009569!4.11e-11!66;UBERON:0003929!4.42e-09!55;UBERON:0005177!1.89e-08!79;UBERON:0002368!5.53e-08!60;UBERON:0004921!5.83e-08!114;UBERON:0001007!1.02e-07!116;UBERON:0001555!1.02e-07!116;UBERON:0007026!1.02e-07!116;UBERON:0004119!1.74e-07!118;UBERON:0000925!1.74e-07!118;UBERON:0006595!1.74e-07!118;UBERON:0002530!4.63e-07!65;UBERON:0000490!6.80e-07!66;UBERON:0002100!8.12e-07!90
|tfbs_overrepresentation_for_novel_motifs=0.515529,0.00410746,0.728967,0.349251,0.583983,0.375236,0.260823,0.823006,0.447161,0.00651839,0.058307,0.0703742,0.824565,0.0803677,0.417765,0,0.181863,1.10569,0.0219362,0.00882429,0.602659,0.285306,0.274124,0.83903,0.101074,0.0925036,0.322089,0.414175,0.295887,0.0229187,0.0448989,0.24825,0.18985,0.256257,0.040001,0.00119992,0.00451793,0.520947,0.431027,0.0417929,0.200539,0.17646,0.945329,0.658424,0.137084,0.329715,0.135497,0.0547326,0.562277,0.0551802,0.171222,0.105162,0.400161,0.352629,0.366252,0.0834375,1.15223,0.232739,0.0954774,0.281271,0.234502,0.109786,0.0959606,0.164496,0.297184,1.05559,0.477375,0.788774,0.654013,0.653981,0.0824089,1.13178,0.00934995,1.01803,0.000428747,0.0109354,0.0811141,0.405602,0.222945,0.190275,0.0797817,0.1927,0.715974,0.241579,0.303733,1.47216e-06,7.97601,0.0229891,0.138179,0.941399,0.536923,0.307432,1.31685,0.386793,0.0581172,0.358256,0.39942,0.259153,0.135636,0.0732502,0.174367,0.248056,0.339171,0.17158,0.509637,0.176029,0.208361,0.19722,0.0766307,0.0720256,0.109842,0.340541,0.620554,0.0601818,1.34096,0.0910418,0.00312853,0.355948,1.02955,0.307968,0.397177,0.152285,0.642404,0.404363,0.590426,0.225416,0.964938,0.25244,1.1983,0.22387,0.326211,0.336418,0.451368,0.30026,0.561842,1.05685,0.854146,0.707421,0.519224,2.88875,0.911155,0.481349,0.668927,0.255543,0.167066,2.60525,0.425589,1.25879,0.124145,0.0335534,0.0241889,4.78781e-06,0.353849,0.118078,0.0890431,0.418931,1.15602,1.34182,3.77663,0.0295616,0.527409,0.303098,0.225714,0.262999,0.495286,0.290114,0.1724,0.897275,0.000716212
}}
}}

Revision as of 17:59, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127435382..127435385,-p@chr10:127435382..127435385
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Mm9::chr10:24635298..24635299,-p@chr10:24635298..24635299
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Mm9::chr10:41405791..41405808,-p@chr10:41405791..41405808
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Mm9::chr10:87376350..87376367,+p@chr10:87376350..87376367
+
Mm9::chr11:120391390..120391415,+p@chr11:120391390..120391415
+
Mm9::chr11:16771803..16771819,+p@chr11:16771803..16771819
+
Mm9::chr13:36818295..36818314,-p@chr13:36818295..36818314
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Mm9::chr15:75052967..75052978,+p@chr15:75052967..75052978
+
Mm9::chr17:30730479..30730484,-p@chr17:30730479..30730484
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Mm9::chr18:85040955..85040968,+p@chr18:85040955..85040968
+
Mm9::chr19:32024443..32024455,+p@chr19:32024443..32024455
+
Mm9::chr19:32024502..32024514,+p@chr19:32024502..32024514
+
Mm9::chr2:103294385..103294399,-p@chr2:103294385..103294399
-
Mm9::chr2:103294453..103294474,+p@chr2:103294453..103294474
+
Mm9::chr2:103294506..103294547,-p@chr2:103294506..103294547
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Mm9::chr2:103294708..103294737,-p@chr2:103294708..103294737
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Mm9::chr2:103294775..103294782,-p@chr2:103294775..103294782
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Mm9::chr2:103294788..103294845,-p@chr2:103294788..103294845
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Mm9::chr2:103294855..103294864,-p@chr2:103294855..103294864
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Mm9::chr2:103307899..103307946,-p@chr2:103307899..103307946
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Mm9::chr3:118787953..118787967,+p@chr3:118787953..118787967
+
Mm9::chr3:118887044..118887048,+p@chr3:118887044..118887048
+
Mm9::chr4:104526380..104526393,-p@chr4:104526380..104526393
-
Mm9::chr4:107777751..107777764,-p@chr4:107777751..107777764
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Mm9::chr4:49557784..49557797,-p@chr4:49557784..49557797
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Mm9::chr4:96309420..96309423,-p@chr4:96309420..96309423
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Mm9::chr5:123630695..123630707,-p@chr5:123630695..123630707
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Mm9::chr5:123631456..123631467,-p@chr5:123631456..123631467
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Mm9::chr5:123631476..123631488,-p@chr5:123631476..123631488
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Mm9::chr5:135599604..135599630,+p@chr5:135599604..135599630
+
Mm9::chr5:146820597..146820625,-p@chr5:146820597..146820625
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Mm9::chr5:146820658..146820666,-p@chr5:146820658..146820666
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Mm9::chr7:134415997..134416003,-p@chr7:134415997..134416003
-
Mm9::chr7:52729831..52729837,-p@chr7:52729831..52729837
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Mm9::chr7:53984058..53984086,-p@chr7:53984058..53984086
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Mm9::chr7:53984116..53984135,-p@chr7:53984116..53984135
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Mm9::chr7:53984241..53984264,-p@chr7:53984241..53984264
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Mm9::chr7:53984353..53984360,-p@chr7:53984353..53984360
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Mm9::chr7:53984532..53984539,-p@chr7:53984532..53984539
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Mm9::chr9:106354410..106354428,+p@chr9:106354410..106354428
+
Mm9::chr9:121823937..121823982,-p@chr9:121823937..121823982
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Mm9::chr9:121824293..121824302,-p@chr9:121824293..121824302
-
Mm9::chrX:20134685..20134694,+p@chrX:20134685..20134694
+


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:0004462lactoylglutathione lyase activity0.00262970470607571
GO:0016846carbon-sulfur lyase activity0.0118310777801947



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
metabolising cell1.20e-085
endopolyploid cell1.20e-085
parenchymal cell1.20e-085
polyploid cell1.20e-085
hepatocyte1.20e-085

Uber Anatomy
Ontology termp-valuen
liver3.44e-2922
epithelial sac3.44e-2922
digestive gland3.44e-2922
epithelium of foregut-midgut junction3.44e-2922
anatomical boundary3.44e-2922
hepatobiliary system3.44e-2922
foregut-midgut junction3.44e-2922
hepatic diverticulum3.44e-2922
liver primordium3.44e-2922
septum transversum3.44e-2922
liver bud3.44e-2922
digestive tract diverticulum1.00e-2723
sac1.00e-2723
exocrine gland3.76e-2525
exocrine system3.76e-2525
abdomen element8.79e-1749
abdominal segment element8.79e-1749
abdominal segment of trunk8.79e-1749
abdomen8.79e-1749
mesenchyme1.90e-1261
entire embryonic mesenchyme1.90e-1261
trunk mesenchyme4.96e-1245
epithelial tube2.44e-1147
subdivision of trunk4.11e-1166
gut epithelium4.42e-0955
trunk region element1.89e-0879
endocrine gland5.53e-0860
subdivision of digestive tract5.83e-08114
digestive system1.02e-07116
digestive tract1.02e-07116
primitive gut1.02e-07116
endoderm-derived structure1.74e-07118
endoderm1.74e-07118
presumptive endoderm1.74e-07118
gland4.63e-0765
unilaminar epithelium6.80e-0766
trunk8.12e-0790


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)

{{{tfbs_overrepresentation_jaspar}}}

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