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Coexpression cluster:C3540: Difference between revisions

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|id=C3540
|id=C3540
|kegg_enrichment=hsa00190;Oxidative_phosphorylation;8.21E-09!hsa05012;Parkinson's_disease;3.22E-08!hsa05016;Huntington's_disease;7.76E-08!hsa05010;Alzheimer's_disease;1.89E-07!hsa04260;Cardiac_muscle_contraction;1.05E-05!hsa01100;Metabolic_pathways;3.35E-05
|kegg_enrichment=hsa00190;Oxidative_phosphorylation;8.21E-09!hsa05012;Parkinson's_disease;3.22E-08!hsa05016;Huntington's_disease;7.76E-08!hsa05010;Alzheimer's_disease;1.89E-07!hsa04260;Cardiac_muscle_contraction;1.05E-05!hsa01100;Metabolic_pathways;3.35E-05
|ontology_enrichment_celltype=CL:0002321!2.04e-10!248;CL:0000220!2.53e-10!246;CL:0000183!7.66e-10!59;CL:0000393!1.90e-08!60;CL:0000211!1.90e-08!60;CL:0000187!7.91e-08!54;CL:0000066!1.27e-07!254;CL:0000680!2.56e-07!57;CL:0000056!2.56e-07!57;CL:0000355!2.56e-07!57;CL:0000222!3.24e-07!119;CL:0000192!5.11e-07!42;CL:0000514!5.11e-07!42
|ontology_enrichment_celltype=CL:0002321!2.41e-10!250;CL:0000183!4.06e-10!59;CL:0000393!7.42e-09!61;CL:0000211!7.42e-09!61;CL:0000187!2.17e-08!55;CL:0000222!6.02e-08!121;CL:0000680!7.95e-08!58;CL:0000056!7.95e-08!58;CL:0000355!7.95e-08!58;CL:0000192!1.19e-07!43;CL:0000514!1.19e-07!43;CL:0000066!7.06e-07!253;CL:0000055!7.09e-07!106
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000481!4.76e-19!347;UBERON:0003104!1.02e-14!238;UBERON:0009142!1.02e-14!238;UBERON:0000483!8.35e-12!309;UBERON:0005256!1.40e-11!143;UBERON:0000119!1.44e-11!312;UBERON:0004290!4.56e-11!70;UBERON:0000475!1.02e-10!365;UBERON:0000914!1.22e-10!83;UBERON:0002329!1.22e-10!83;UBERON:0003077!1.22e-10!83;UBERON:0003059!1.22e-10!83;UBERON:0007282!1.22e-10!83;UBERON:0009618!1.22e-10!83;UBERON:0007285!1.22e-10!83;UBERON:0002100!1.36e-10!216;UBERON:0000486!2.63e-10!82;UBERON:0000064!1.59e-09!219;UBERON:0002385!3.75e-09!63;UBERON:0001015!3.75e-09!63;UBERON:0000383!3.75e-09!63;UBERON:0001134!4.29e-09!61;UBERON:0002036!4.29e-09!61;UBERON:0003082!4.29e-09!61;UBERON:0003914!8.99e-09!118;UBERON:0003103!1.10e-08!69;UBERON:0000025!1.51e-08!194;UBERON:0000922!6.61e-08!612;UBERON:0000477!1.67e-07!286;UBERON:0000923!2.38e-07!604;UBERON:0005291!2.38e-07!604;UBERON:0006598!2.38e-07!604;UBERON:0002532!2.38e-07!604;UBERON:0002050!2.53e-07!605;UBERON:0005423!2.53e-07!605;UBERON:0004111!3.98e-07!241
|ontology_enrichment_uberon=UBERON:0000481!1.18e-18!342;UBERON:0007503!2.94e-14!78;UBERON:0003104!5.74e-14!160;UBERON:0009142!5.74e-14!160;UBERON:0000483!1.72e-12!306;UBERON:0000119!3.88e-12!309;UBERON:0000475!4.00e-12!264;UBERON:0007524!7.55e-12!73;UBERON:0003077!7.80e-12!72;UBERON:0007285!7.80e-12!72;UBERON:0005256!9.01e-12!122;UBERON:0002329!1.33e-11!71;UBERON:0003059!1.33e-11!71;UBERON:0007282!1.33e-11!71;UBERON:0004290!1.33e-11!71;UBERON:0009618!1.33e-11!71;UBERON:0002100!1.64e-11!199;UBERON:0000477!3.78e-11!373;UBERON:0000486!1.77e-10!83;UBERON:0002385!1.19e-09!64;UBERON:0001015!1.19e-09!64;UBERON:0000383!1.19e-09!64;UBERON:0001134!1.21e-09!62;UBERON:0002036!1.21e-09!62;UBERON:0003082!1.21e-09!62;UBERON:0000490!1.62e-09!148;UBERON:0000064!3.86e-09!218;UBERON:0003914!4.23e-09!117;UBERON:0000025!2.22e-08!192;UBERON:0003103!6.33e-08!68;UBERON:0000922!1.24e-07!592;UBERON:0004111!3.28e-07!240
|pathway_enrichment=9.66492387457841e-08;1.52947420315203e-05;3;132;Oxidative phosphorylation (KEGG):00190!6.31961929821581e-05;0.00444479890641179;3;1138;Metabolic pathways (KEGG):01100!2.15074464693702e-05;0.00170177670188892;2;77;Cardiac muscle contraction (KEGG):04260!1.96661053766193e-07;2.48972894068001e-05;3;167;Alzheimer's disease (KEGG):05010!9.22896270049956e-08;1.52947420315203e-05;3;130;Parkinson's disease (KEGG):05012!2.59185625084851e-07;2.73440834464518e-05;3;183;Huntington's disease (KEGG):05016!5.41556645674944e-08;1.52947420315203e-05;3;109;Electron Transport Chain (Wikipathways):WP111!2.20095901611869e-08;1.39320705720313e-05;3;81;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Reactome):REACT_6305!3.42164256458367e-06;0.000309414249054495;2;31;{CYCS,35} (Static Module):NA
|pathway_enrichment=9.66492387457841e-08;1.52947420315203e-05;3;132;Oxidative phosphorylation (KEGG):00190!6.31961929821581e-05;0.00444479890641179;3;1138;Metabolic pathways (KEGG):01100!2.15074464693702e-05;0.00170177670188892;2;77;Cardiac muscle contraction (KEGG):04260!1.96661053766193e-07;2.48972894068001e-05;3;167;Alzheimer's disease (KEGG):05010!9.22896270049956e-08;1.52947420315203e-05;3;130;Parkinson's disease (KEGG):05012!2.59185625084851e-07;2.73440834464518e-05;3;183;Huntington's disease (KEGG):05016!5.41556645674944e-08;1.52947420315203e-05;3;109;Electron Transport Chain (Wikipathways):WP111!2.20095901611869e-08;1.39320705720313e-05;3;81;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Reactome):REACT_6305!3.42164256458367e-06;0.000309414249054495;2;31;{CYCS,35} (Static Module):NA
|tf_chipseq_enrich=CTCFL#140690;2:13.1643162393162:0.00743336703699601:0.0306754156779211!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324694781804275!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321507180643085!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.031998918599741!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461316727954534!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00761152113762452!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269213988173359!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460343334816001!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470547164388949!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172679465127204!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276116509777606!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457300202120404!STAT1#6772;2:13.8043916647995:0.00677093170844408:0.0287494140219617!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.0054185026445323!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328728570954589
|tf_chipseq_enrich=CTCFL#140690;2:13.1643162393162:0.00743336703699601:0.0306754156779211!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324694781804275!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321507180643085!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.031998918599741!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461316727954534!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00761152113762452!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269213988173359!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460343334816001!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470547164388949!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172679465127204!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276116509777606!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457300202120404!STAT1#6772;2:13.8043916647995:0.00677093170844408:0.0287494140219617!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.0054185026445323!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328728570954589
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}}
}}

Revision as of 15:11, 19 October 2012


Full id: C3540_skeletal_left_heart_Mesenchymal_diaphragm_Alveolar_tongue



Phase1 CAGE Peaks

Hg19::chr16:2009500..2009584,+p1@NDUFB10
Hg19::chr2:98262497..98262549,+p1@COX5B
Hg19::chr3:48647059..48647102,-p1@UQCRC1


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


p.valueFDRnGenesnPathwayName
9.66492387457841e-081.52947420315203e-053132Oxidative phosphorylation (KEGG):00190
6.31961929821581e-050.0044447989064117931138Metabolic pathways (KEGG):01100
2.15074464693702e-050.00170177670188892277Cardiac muscle contraction (KEGG):04260
1.96661053766193e-072.48972894068001e-053167Alzheimer's disease (KEGG):05010
9.22896270049956e-081.52947420315203e-053130Parkinson's disease (KEGG):05012
2.59185625084851e-072.73440834464518e-053183Huntington's disease (KEGG):05016
5.41556645674944e-081.52947420315203e-053109Electron Transport Chain (Wikipathways):WP111
2.20095901611869e-081.39320705720313e-05381Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Reactome):REACT_6305
3.42164256458367e-060.000309414249054495231{CYCS,35} (Static Module):NA



Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


GO IDGO nameFDR corrected p-value
GO:0005743mitochondrial inner membrane3.94167936296023e-05
GO:0019866organelle inner membrane3.94167936296023e-05
GO:0031966mitochondrial membrane4.39079275427809e-05
GO:0005740mitochondrial envelope4.39079275427809e-05
GO:0044429mitochondrial part7.57771798962151e-05
GO:0031967organelle envelope7.57771798962151e-05
GO:0031975envelope7.57771798962151e-05
GO:0006118electron transport0.000104063478946275
GO:0005746mitochondrial respiratory chain0.000141381126508339
GO:0006091generation of precursor metabolites and energy0.000180464480492059
GO:0005739mitochondrion0.000198827660296956
GO:0044455mitochondrial membrane part0.000269873470898099
GO:0006119oxidative phosphorylation0.000430686169885607
GO:0031090organelle membrane0.00053948090000896
GO:0016491oxidoreductase activity0.000549886679035116
GO:0015078hydrogen ion transmembrane transporter activity0.000570691170457736
GO:0015077monovalent inorganic cation transmembrane transporter activity0.000619459136717262
GO:0022890inorganic cation transmembrane transporter activity0.000924073405410639
GO:0044446intracellular organelle part0.00772108058328133
GO:0044422organelle part0.00772108058328133
GO:0008324cation transmembrane transporter activity0.00792935597784679
GO:0016681oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor0.00822131044074366
GO:0008121ubiquinol-cytochrome-c reductase activity0.00822131044074366
GO:0016679oxidoreductase activity, acting on diphenols and related substances as donors0.00822131044074366
GO:0044444cytoplasmic part0.00846379679961598
GO:0007585respiratory gaseous exchange0.00846379679961598
GO:0045271respiratory chain complex I0.0103427143324249
GO:0030964NADH dehydrogenase complex (quinone)0.0103427143324249
GO:0005747mitochondrial respiratory chain complex I0.0103427143324249
GO:0004129cytochrome-c oxidase activity0.0103427143324249
GO:0016675oxidoreductase activity, acting on heme group of donors0.0103427143324249
GO:0016676oxidoreductase activity, acting on heme group of donors, oxygen as acceptor0.0103427143324249
GO:0015002heme-copper terminal oxidase activity0.0103427143324249
GO:0015075ion transmembrane transporter activity0.0110499762773029
GO:0009060aerobic respiration0.0110499762773029
GO:0006120mitochondrial electron transport, NADH to ubiquinone0.0113739705753752
GO:0016310phosphorylation0.0114123006757427
GO:0045333cellular respiration0.0115721504980818
GO:0022891substrate-specific transmembrane transporter activity0.0128118673586426
GO:0008137NADH dehydrogenase (ubiquinone) activity0.0128118673586426
GO:0003954NADH dehydrogenase activity0.0128118673586426
GO:0050136NADH dehydrogenase (quinone) activity0.0128118673586426
GO:0042775organelle ATP synthesis coupled electron transport0.0128469912276672
GO:0016655oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor0.0128469912276672
GO:0022857transmembrane transporter activity0.0128469912276672
GO:0042773ATP synthesis coupled electron transport0.0128484456315034
GO:0006793phosphorus metabolic process0.0129587858695853
GO:0006796phosphate metabolic process0.0129587858695853
GO:0022892substrate-specific transporter activity0.013728668980004
GO:0016651oxidoreductase activity, acting on NADH or NADPH0.016352482504285
GO:0015980energy derivation by oxidation of organic compounds0.017363226964559
GO:0005737cytoplasm0.0176623737467382
GO:0004222metalloendopeptidase activity0.0274222150223631
GO:0043231intracellular membrane-bound organelle0.0274222150223631
GO:0043227membrane-bound organelle0.0274222150223631
GO:0009055electron carrier activity0.0340569250592044
GO:0016020membrane0.0356268822602444
GO:0043229intracellular organelle0.0464093602139209
GO:0043226organelle0.0464093602139209
GO:0008237metallopeptidase activity0.0471924897371985



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>


Uber Anatomy
Ontology termp-valuen
multi-tissue structure1.18e-18342
epithelial vesicle2.94e-1478
mesenchyme5.74e-14160
entire embryonic mesenchyme5.74e-14160
epithelium1.72e-12306
cell layer3.88e-12309
organism subdivision4.00e-12264
dense mesenchyme tissue7.55e-1273
paraxial mesoderm7.80e-1272
presumptive paraxial mesoderm7.80e-1272
trunk mesenchyme9.01e-12122
somite1.33e-1171
presomitic mesoderm1.33e-1171
presumptive segmental plate1.33e-1171
dermomyotome1.33e-1171
trunk paraxial mesoderm1.33e-1171
trunk1.64e-11199
anatomical cluster3.78e-11373
multilaminar epithelium1.77e-1083
muscle tissue1.19e-0964
musculature1.19e-0964
musculature of body1.19e-0964
skeletal muscle tissue1.21e-0962
striated muscle tissue1.21e-0962
myotome1.21e-0962
unilaminar epithelium1.62e-09148
organ part3.86e-09218
epithelial tube4.23e-09117
tube2.22e-08192
compound organ6.33e-0868
embryo1.24e-07592
anatomical conduit3.28e-07240


Overrepresented TFBS (DNA) motifs on this co-expression cluster<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}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCFL#140690213.16431623931620.007433367036996010.0306754156779211
E2F1#186934.907389214879320.008460985347239390.0324694781804275
E2F6#187635.017155731697390.00791769806886330.0321507180643085
EGR1#195834.988179094810140.008056488137383440.031998918599741
ELF1#199734.258097958807540.01295179875054610.0461316727954534
ETS1#211339.728760922202340.001085840092584840.00761152113762452
NFKB1#479035.488063424193840.006049381815655430.0269213988173359
NR3C1#290829.982015554115360.01278474365547170.0460343334816001
NRF1#4899312.21027944771090.0005492172401020010.00470547164388949
PAX5#507936.669565531177830.003370290999677260.0172679465127204
SIN3A#2594235.408884726815140.006318961977991520.0276116509777606
SMC3#9126210.02995522995520.0126656379767470.0457300202120404
STAT1#6772213.80439166479950.006770931708444080.0287494140219617
TAF7#6879311.43306940492390.0006690181981945830.0054185026445323
YY1#752834.911170749853860.008441455341808260.0328728570954589



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.