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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0.13619218658599,0,0,0,0.788223334421264,1.14933328872533,0.582592648074115,0.717138012664496,0,0,0,0,0,0,0,0.0403133681301215,0,0,0,0,0,0,0,0,0,0.0312564193926682,0,0.343373863650849,0.359204935882496,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.184737966471201,0.262448778918228,0,0,0,0,0,0.0918192515358666,0.405253361266419,0.381179465482496,0.027549189648299,0.0674541896311435,0.136969166919767,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0735024167162535,0,0,0,0,0.0185736976508778,0,0.0231717684481141,0,0,0.0365294005496895,0,0,0.157182883491893,0.149856467963095,0,0,0,0.0659164972702785,0.575399717404365,0,0.323540090673018,0,0.0792454678815347,0.142123828884131,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.117589695957107,0,0,0,0,0,0,0.162483374261274,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0340113632754165,0.109331033040409,0.104741781954859,0.109512603169101,0.206790410972571,0.0540496261796572,0.214323636893302,0.261583765506141,0.328728904736635,0.13512544777972,0,0,0,0,0,0.460971273427128,0.379520716834596,0.466584160215191,0.4737978803031,0.317646815134236,0.229243569897871,0.345075950201752,0.356661223434894,0.435299439465814,0,0,0.454028727012301,0.392712270020621,0.355556938823921,0.148642435742889,0.270191966560285,0,0.414294300096539,0.128119866952565,0.0452252653904662,0.163579048641079,0,0.106451101971206,0,0,0.387979180422312,0,0.260515205681245,0,0,0,1.23539337516382,1.13895495535548,0,0,0,0,0.0966155181422749,0.153913991558631,0.0874537470001215,0.110803081130275,0.140942333732381,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.198767439340487,0,0,0.102412476390192,0,0,0,0,0.109226104830221,0,0.130421960234778,0,0.116597576933876,0.253326341486756,0.3713731029035,0.558060289409772,0.673670302236212,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.172477148294184,0,0,0,0,0,0,0,0.0367435466625445,0,0,0,0,0,0,0.510776048834566,0.530975180707586,0.606244358672607,0,0,0,0,0,0.0647775726819609,0,0,0,0,0,0,0.387098125502125,0.480722760342793,0.121061146072473,0.0878725470806415,0.0363254862571286,0,0.447901659000403,0.43027448877689,0.409713307665968,0.195590414110735,0.152962663947244,0,0.0341103214948521,0.150897135082807,0,0.258359310587411,0.287699985862175,0.423841595182883,0.772943937615838,0.389632539296021,0,0,0.139477774314491,0.392807403603684,0.217683092140345,0.0991786544889834,0.0190256891830726,0,0,0,0,0,0,0,0,0,0,0,0,0.149463547883141,0.141255358724553,0.0521599633818348,0.177764092626202,0,0,0,0,0,0,0,0.0290468398958313,0,0.11938108556327,0.51687399512607,0,0,0,0,0,0.183142341098309,0.166289478448155,0,0,0,0,0,0,0,0.057439935027299,0,0,0,0,0,0,0.147929950453612,0.378250483909299,0.565069283936436,0.155407115211377,0.173549060254662,0.183159322676958,0,0,0,0,0,0.076438074802024,0.222795072775063,0.502129252619316,0.108034143853115,0.212619186992201,0.214449074965237,0.0796978867763615,0.0898074372339897,0,0,0,0,0,0,0,0,0.39716401256961,0.379462547880388,0.206269694716997,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0533344296716605,0,0,0,0,0.284799500901645,0,0,0,0.495238463861848,0.550809254477056,0.395295528955579,0.245813174782655,0,0,0.0458347162451775,0,0.0415945576318429,0,0.105947296040957,0.0975809997847489,0,0,0,0.35063654883701,0.316835355032157,0,0,0,0,0,0,0,0.791456847772767,0.0532107939468775,0,0.210818117052445,0.402351139140505,0.646015681118312,0,0,0,0,0,0,0,0,0,0,0.056685265411804,0.00790199227215325,0,0.256066180324698,0.385854704702773,0.660885553118884,0.848867566773544,0.3569818409289,0.965082337652823,0,0,0,0,0,0.125690448946222,0,0,0.556184832362907,0.482775635457649,0.460404196046656,0,0.299999916441319,0.0368115019473605,0.207103666835013,0,0,0,0,0,0,0,0.172002578627489,0.410813158394845,0.0722224018548135,0.344374029099016,0,0,0.0304099808375785,0.0802352392975896,0,0.1241754307343,0,0,0.195683583376492,0,1.08615667378128,0.0948261398824531,0.143353834976781,0.156597065690446,0,0.260497498517127,0.135274715749039,0.269077096199849,0.0201011396294926,0.145027106951467,0.0148503541200765,0.105198010485346,0.0393578995913525,0,0.3745393357846,0.215180180019106,0.358071584125933,1.06382172517721,0.286736431953177,0,0.098457478620693,0.0584468268118252,0.0963903106919151,0.162082679775905,0.0798817004452529,0.167253085067442,0,0,0,0,0,0.25748340328648,0,0,0,0,0.567534236483099,0,0,0,0,0.335449775449978,0.212258326954079,0.314885882960437,0.240582703685912,0.328654351499985,0,0,0,0.287360951778888,0.274789530703325,0.343914577960663,0,0,0,0,0.105582174569955,0.0327649730749157,0.0832161034844002,0.277938350467095,0.194240896833933,0,0,0.40015433764568,0,0,0,0,0,0,0.023308462951519,0.13494627757195,0,0,0,0.456604378952243,0,0.0220321056448849,0,0.0752614132322225,0,0,0,0,0,0,0,0,0.118631122812508,0,0,0,0,0,0,0,0.0511449590802371,0,0,0.441222069591838,0,0.0846560328614142,0,0,0,0,0,0,0,0.0305812234382831,0,0,0.06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|full_id=C819_Alveolar_MCF7_mesothelioma_endometrioid_signet_Renal_gastric
|full_id=C819_Alveolar_MCF7_mesothelioma_endometrioid_signet_Renal_gastric
|gostat_on_coexpression_clusters=GO:0005882!intermediate filament!0.00163391453254799!3856;3875$GO:0045111!intermediate filament cytoskeleton!0.00163391453254799!3856;3875$GO:0043000!Golgi to plasma membrane CFTR protein transport!0.00266882527361085!3875$GO:0043001!Golgi to plasma membrane protein transport!0.0030023842411101!3875$GO:0006893!Golgi to plasma membrane transport!0.00560412061869646!3875$GO:0044430!cytoskeletal part!0.00756000214426228!3856;3875$GO:0030018!Z disc!0.00756000214426228!3856$GO:0042383!sarcolemma!0.00756000214426228!3856$GO:0031674!I band!0.00756000214426228!3856$GO:0006892!post-Golgi vesicle-mediated transport!0.00840444861332212!3875$GO:0005856!cytoskeleton!0.0107478076253176!3856;3875$GO:0030017!sarcomere!0.0160021099440816!3856$GO:0030016!myofibril!0.0163086417198209!3856$GO:0044449!contractile fiber part!0.0170648948467576!3856$GO:0043292!contractile fiber!0.0170648948467576!3856$GO:0005200!structural constituent of cytoskeleton!0.0197684410496945!3875$GO:0045095!keratin filament!0.0197684410496945!3875$GO:0048193!Golgi vesicle transport!0.0197684410496945!3875$GO:0043232!intracellular non-membrane-bound organelle!0.0251111392713346!3856;3875$GO:0043228!non-membrane-bound organelle!0.0251111392713346!3856;3875$GO:0016043!cellular component organization and biogenesis!0.0301217712229689!3856;3875$GO:0051707!response to other organism!0.0372143670088532!3856$GO:0043066!negative regulation of apoptosis!0.0372143670088532!3875$GO:0043069!negative regulation of programmed cell death!0.0372143670088532!3875$GO:0045045!secretory pathway!0.0372143670088532!3875$GO:0044446!intracellular organelle part!0.0372143670088532!3856;3875$GO:0044422!organelle part!0.0372143670088532!3856;3875$GO:0009607!response to biotic stimulus!0.0408206615432263!3856$GO:0032940!secretion by cell!0.0408206615432263!3875$GO:0051704!multi-organism process!0.0442194544953417!3856$GO:0046903!secretion!0.0493096828301634!3875
|gostat_on_coexpression_clusters=GO:0005882!intermediate filament!0.00163391453254799!3856;3875$GO:0045111!intermediate filament cytoskeleton!0.00163391453254799!3856;3875$GO:0043000!Golgi to plasma membrane CFTR protein transport!0.00266882527361085!3875$GO:0043001!Golgi to plasma membrane protein transport!0.0030023842411101!3875$GO:0006893!Golgi to plasma membrane transport!0.00560412061869646!3875$GO:0044430!cytoskeletal part!0.00756000214426228!3856;3875$GO:0030018!Z disc!0.00756000214426228!3856$GO:0042383!sarcolemma!0.00756000214426228!3856$GO:0031674!I band!0.00756000214426228!3856$GO:0006892!post-Golgi vesicle-mediated transport!0.00840444861332212!3875$GO:0005856!cytoskeleton!0.0107478076253176!3856;3875$GO:0030017!sarcomere!0.0160021099440816!3856$GO:0030016!myofibril!0.0163086417198209!3856$GO:0044449!contractile fiber part!0.0170648948467576!3856$GO:0043292!contractile fiber!0.0170648948467576!3856$GO:0005200!structural constituent of cytoskeleton!0.0197684410496945!3875$GO:0045095!keratin filament!0.0197684410496945!3875$GO:0048193!Golgi vesicle transport!0.0197684410496945!3875$GO:0043232!intracellular non-membrane-bound organelle!0.0251111392713346!3856;3875$GO:0043228!non-membrane-bound organelle!0.0251111392713346!3856;3875$GO:0016043!cellular component organization and biogenesis!0.0301217712229689!3856;3875$GO:0051707!response to other organism!0.0372143670088532!3856$GO:0043066!negative regulation of apoptosis!0.0372143670088532!3875$GO:0043069!negative regulation of programmed cell death!0.0372143670088532!3875$GO:0045045!secretory pathway!0.0372143670088532!3875$GO:0044446!intracellular organelle part!0.0372143670088532!3856;3875$GO:0044422!organelle part!0.0372143670088532!3856;3875$GO:0009607!response to biotic stimulus!0.0408206615432263!3856$GO:0032940!secretion by cell!0.0408206615432263!3875$GO:0051704!multi-organism process!0.0442194544953417!3856$GO:0046903!secretion!0.0493096828301634!3875

Revision as of 18:33, 12 September 2012


Full id: C819_Alveolar_MCF7_mesothelioma_endometrioid_signet_Renal_gastric



Phase1 CAGE Peaks

Hg19::chr12:53298570..53298600,-p5@KRT8
Hg19::chr12:53298672..53298713,-p7@KRT8
Hg19::chr12:53342893..53342911,+p1@KRT18
Hg19::chr12:53343121..53343150,+p6@KRT18
Hg19::chr12:53344588..53344613,+p4@KRT18
Hg19::chr12:53344624..53344654,-p@chr12:53344624..53344654
-
Hg19::chr12:53345928..53345949,+p3@KRT18
Hg19::chr2:203706578..203706583,-p1@KRT8P15
Hg19::chr2:236715167..236715174,+p@chr2:236715167..236715174
+
Hg19::chr3:170213152..170213154,+p1@KRT8P13


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

No results for this coexpression

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:0005882intermediate filament0.00163391453254799
GO:0045111intermediate filament cytoskeleton0.00163391453254799
GO:0043000Golgi to plasma membrane CFTR protein transport0.00266882527361085
GO:0043001Golgi to plasma membrane protein transport0.0030023842411101
GO:0006893Golgi to plasma membrane transport0.00560412061869646
GO:0044430cytoskeletal part0.00756000214426228
GO:0030018Z disc0.00756000214426228
GO:0042383sarcolemma0.00756000214426228
GO:0031674I band0.00756000214426228
GO:0006892post-Golgi vesicle-mediated transport0.00840444861332212
GO:0005856cytoskeleton0.0107478076253176
GO:0030017sarcomere0.0160021099440816
GO:0030016myofibril0.0163086417198209
GO:0044449contractile fiber part0.0170648948467576
GO:0043292contractile fiber0.0170648948467576
GO:0005200structural constituent of cytoskeleton0.0197684410496945
GO:0045095keratin filament0.0197684410496945
GO:0048193Golgi vesicle transport0.0197684410496945
GO:0043232intracellular non-membrane-bound organelle0.0251111392713346
GO:0043228non-membrane-bound organelle0.0251111392713346
GO:0016043cellular component organization and biogenesis0.0301217712229689
GO:0051707response to other organism0.0372143670088532
GO:0043066negative regulation of apoptosis0.0372143670088532
GO:0043069negative regulation of programmed cell death0.0372143670088532
GO:0045045secretory pathway0.0372143670088532
GO:0044446intracellular organelle part0.0372143670088532
GO:0044422organelle part0.0372143670088532
GO:0009607response to biotic stimulus0.0408206615432263
GO:0032940secretion by cell0.0408206615432263
GO:0051704multi-organism process0.0442194544953417
GO:0046903secretion0.0493096828301634



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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell7.29e-57254
embryonic cell8.26e-18248
endodermal cell4.19e-1659
squamous epithelial cell3.86e-1362
mesothelial cell2.27e-1119
endo-epithelial cell2.88e-1143
mesodermal cell6.90e-08119
lining cell1.29e-0757
barrier cell1.29e-0757
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.01e-24169
endoderm1.01e-24169
presumptive endoderm1.01e-24169
immaterial anatomical entity1.85e-22126
subdivision of digestive tract4.26e-22129
endodermal part of digestive tract4.26e-22129
primordium8.58e-21168
mesenchyme9.41e-21238
entire embryonic mesenchyme9.41e-21238
digestive system1.18e-20155
digestive tract1.18e-20155
primitive gut1.18e-20155
mixed endoderm/mesoderm-derived structure8.09e-20130
trunk region element7.91e-18107
subdivision of trunk1.49e-17113
endo-epithelium3.77e-1782
foregut1.45e-1698
multi-tissue structure6.12e-16347
anatomical space7.96e-16104
trunk1.17e-15216
epithelial tube8.29e-15118
abdomen element9.38e-1355
abdominal segment element9.38e-1355
abdominal segment of trunk2.34e-1261
abdomen2.34e-1261
unilaminar epithelium1.01e-11138
gut epithelium3.52e-1154
anatomical cavity1.62e-1070
respiratory primordium2.05e-1038
endoderm of foregut2.05e-1038
urinary system structure2.17e-1044
renal system3.34e-1045
body cavity precursor9.36e-1063
cell layer1.45e-09312
anatomical cluster1.77e-09286
organ segment1.99e-0997
sac2.23e-0926
epithelium2.33e-09309
epithelial sac2.34e-0925
respiratory tract2.63e-0953
epithelium of foregut-midgut junction4.53e-0925
anatomical boundary4.53e-0925
hepatobiliary system4.53e-0925
foregut-midgut junction4.53e-0925
septum transversum4.53e-0925
duct5.36e-0926
reproductive structure1.09e-0859
reproductive system1.09e-0859
segment of respiratory tract1.68e-0846
multi-cellular organism1.78e-08659
respiratory system2.01e-0872
extraembryonic membrane2.03e-0814
membranous layer2.03e-0814
intermediate mesoderm3.15e-0837
anatomical conduit4.38e-08241
epithelial bud5.56e-0837
gland6.24e-0859
digestive tract diverticulum7.38e-0823
hepatic diverticulum7.95e-0822
liver primordium7.95e-0822
kidney8.27e-0827
kidney mesenchyme8.27e-0827
kidney rudiment8.27e-0827
kidney field8.27e-0827
organism subdivision8.79e-08365
organ part9.43e-08219
trunk mesenchyme1.26e-07143
compound organ1.46e-0769
exocrine gland2.71e-0731
exocrine system2.71e-0731
epithelial fold5.23e-0751
reproductive organ5.85e-0748
mesoderm6.57e-07448
mesoderm-derived structure6.57e-07448
presumptive mesoderm6.57e-07448
endocrine system9.56e-0745
Disease
Ontology termp-valuen
carcinoma3.22e-29106
cell type cancer3.99e-25143
cancer2.83e-13235
disease of cellular proliferation7.75e-13239
adenocarcinoma7.16e-1025


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
GTF2F1#296245.095864350703060.00541638888230090.02456817539538
TAF7#687944.573227761969570.007980040641138020.0322633735103675
TFAP2A#702046.607453749217980.002096541917954080.0121254148504378
TFAP2C#702244.323691443944090.009735325145753660.0366118477151477



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.

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