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Coexpression cluster:C3206: Difference between revisions

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|full_id=C3206_Mesenchymal_Osteoblast_tenocyte_Synoviocyte_Alveolar_Fibroblast_Smooth
|full_id=C3206_Mesenchymal_Osteoblast_tenocyte_Synoviocyte_Alveolar_Fibroblast_Smooth
|id=C3206
|id=C3206
|ontology_enrichment_celltype=CL:0000055!1.38e-38!180;CL:0000222!1.65e-24!119;CL:0000220!4.30e-21!246;CL:0002321!7.04e-21!248;CL:0000548!1.11e-19!679;CL:0000004!1.11e-19!679;CL:0000255!1.11e-19!679;CL:0000057!5.59e-19!75;CL:0000012!5.72e-19!682;CL:0000183!6.20e-18!59;CL:0000680!4.95e-17!57;CL:0000056!4.95e-17!57;CL:0000355!4.95e-17!57;CL:0000144!5.31e-17!625;CL:0002371!1.03e-16!591;CL:0000187!8.41e-16!54;CL:0000192!5.14e-14!42;CL:0000514!5.14e-14!42;CL:0000393!2.40e-13!60;CL:0000211!2.40e-13!60;CL:0000359!3.24e-10!32;CL:0000213!1.14e-07!57;CL:0000215!1.14e-07!57;CL:0000066!1.88e-07!254;CL:0000003!2.77e-07!722;CL:0002620!9.25e-07!23
|ontology_enrichment_celltype=CL:0000222!9.88e-25!121;CL:0002321!1.26e-20!250;CL:0000548!1.04e-19!679;CL:0000255!1.04e-19!679;CL:0000057!4.20e-19!76;CL:0000055!1.91e-18!106;CL:0000183!6.91e-18!59;CL:0000680!2.00e-17!58;CL:0000056!2.00e-17!58;CL:0000355!2.00e-17!58;CL:0002371!2.38e-16!588;CL:0000187!3.97e-16!55;CL:0000192!4.25e-14!43;CL:0000514!4.25e-14!43;CL:0000393!1.18e-13!61;CL:0000211!1.18e-13!61;CL:0000359!5.99e-10!32;CL:0000213!1.18e-07!58;CL:0000215!1.18e-07!58;CL:0000066!1.54e-07!253;CL:0000003!4.04e-07!722;CL:0002078!8.26e-07!45
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005256!1.13e-19!143;UBERON:0000914!8.43e-19!83;UBERON:0002329!8.43e-19!83;UBERON:0003077!8.43e-19!83;UBERON:0003059!8.43e-19!83;UBERON:0007282!8.43e-19!83;UBERON:0009618!8.43e-19!83;UBERON:0007285!8.43e-19!83;UBERON:0004290!2.93e-18!70;UBERON:0002100!1.23e-17!216;UBERON:0000486!2.20e-17!82;UBERON:0003104!2.21e-16!238;UBERON:0009142!2.21e-16!238;UBERON:0001134!6.94e-16!61;UBERON:0002036!6.94e-16!61;UBERON:0003082!6.94e-16!61;UBERON:0002385!3.83e-15!63;UBERON:0001015!3.83e-15!63;UBERON:0000383!3.83e-15!63;UBERON:0002049!4.37e-15!79;UBERON:0007798!4.37e-15!79;UBERON:0000490!1.85e-14!138;UBERON:0003914!4.18e-14!118;UBERON:0000055!8.20e-12!69;UBERON:0004872!1.02e-11!84;UBERON:0000926!1.65e-11!448;UBERON:0004120!1.65e-11!448;UBERON:0006603!1.65e-11!448;UBERON:0001981!1.14e-10!60;UBERON:0007500!1.14e-10!60;UBERON:0004537!1.14e-10!60;UBERON:0006965!1.14e-10!60;UBERON:0001637!2.64e-10!42;UBERON:0003509!2.64e-10!42;UBERON:0004572!2.64e-10!42;UBERON:0000475!7.63e-10!365;UBERON:0000481!1.09e-09!347;UBERON:0000468!3.62e-09!659;UBERON:0004535!5.91e-09!110;UBERON:0000119!1.04e-08!312;UBERON:0004573!1.72e-08!33;UBERON:0004571!1.72e-08!33;UBERON:0001009!2.00e-08!113;UBERON:0000483!2.57e-08!309;UBERON:0003102!2.96e-08!95;UBERON:0000467!6.65e-08!625;UBERON:0000480!1.07e-07!626;UBERON:0002199!6.80e-07!45;UBERON:0002416!6.80e-07!45
|ontology_enrichment_uberon=UBERON:0007503!3.72e-21!78;UBERON:0002329!1.54e-18!71;UBERON:0003059!1.54e-18!71;UBERON:0007282!1.54e-18!71;UBERON:0004290!1.54e-18!71;UBERON:0009618!1.54e-18!71;UBERON:0007524!2.59e-18!73;UBERON:0000486!7.46e-18!83;UBERON:0003077!9.49e-18!72;UBERON:0007285!9.49e-18!72;UBERON:0003104!1.54e-17!160;UBERON:0009142!1.54e-17!160;UBERON:0000490!9.74e-17!148;UBERON:0005256!1.47e-16!122;UBERON:0001134!1.94e-16!62;UBERON:0002036!1.94e-16!62;UBERON:0003082!1.94e-16!62;UBERON:0002100!2.36e-16!199;UBERON:0000475!4.51e-16!264;UBERON:0002385!1.54e-15!64;UBERON:0001015!1.54e-15!64;UBERON:0000383!1.54e-15!64;UBERON:0002049!6.07e-15!78;UBERON:0007798!6.07e-15!78;UBERON:0003914!1.17e-13!117;UBERON:0004872!1.10e-11!83;UBERON:0000055!2.61e-11!68;UBERON:0007500!3.91e-10!59;UBERON:0001981!3.91e-10!59;UBERON:0004537!3.91e-10!59;UBERON:0006965!3.91e-10!59;UBERON:0001637!4.89e-10!42;UBERON:0003509!4.89e-10!42;UBERON:0004572!4.89e-10!42;UBERON:0004535!4.09e-09!109;UBERON:0001009!1.19e-08!112;UBERON:0000119!1.83e-08!309;UBERON:0000468!3.93e-08!656;UBERON:0000483!4.43e-08!306;UBERON:0004573!4.63e-08!33;UBERON:0004571!4.63e-08!33;UBERON:0003102!9.90e-08!99;UBERON:0000481!1.65e-07!342;UBERON:0000467!1.94e-07!624;UBERON:0000480!3.04e-07!625;UBERON:0000926!7.43e-07!315;UBERON:0004120!7.43e-07!315;UBERON:0006603!7.43e-07!315;UBERON:0002199!8.09e-07!46;UBERON:0002416!8.09e-07!46
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189294786270692!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0114979992118716!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323861773384766!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.0043583338561804!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320696710728724!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319272810419742!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460327687496438!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0166973700387824!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00760284616716732!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00579848165624099!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00390057707080082!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127687072894867!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156241141988736!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185871447873024!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00718569973869471!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00469699470512716!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172400363283192!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136191457829515!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00879903852888776!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275597623828387!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00239093076762209!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245587424656941!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.0054088552098811!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00612071068851368!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189624772528837!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328129058524309!ZBTB33#10009;3:31.6647250299812:3.14815888737575e-05:0.00063314185641948!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.013969553784394!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.0024213782189318
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}}
}}

Revision as of 14:53, 19 October 2012


Full id: C3206_Mesenchymal_Osteoblast_tenocyte_Synoviocyte_Alveolar_Fibroblast_Smooth



Phase1 CAGE Peaks

Hg19::chr11:842826..842881,+p1@TSPAN4
Hg19::chr11:842903..842923,+p5@TSPAN4
Hg19::chr11:842928..842980,+p3@TSPAN4


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

No GOStat results

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
epithelial vesicle3.72e-2178
somite1.54e-1871
presomitic mesoderm1.54e-1871
presumptive segmental plate1.54e-1871
dermomyotome1.54e-1871
trunk paraxial mesoderm1.54e-1871
dense mesenchyme tissue2.59e-1873
multilaminar epithelium7.46e-1883
paraxial mesoderm9.49e-1872
presumptive paraxial mesoderm9.49e-1872
mesenchyme1.54e-17160
entire embryonic mesenchyme1.54e-17160
unilaminar epithelium9.74e-17148
trunk mesenchyme1.47e-16122
skeletal muscle tissue1.94e-1662
striated muscle tissue1.94e-1662
myotome1.94e-1662
trunk2.36e-16199
organism subdivision4.51e-16264
muscle tissue1.54e-1564
musculature1.54e-1564
musculature of body1.54e-1564
vasculature6.07e-1578
vascular system6.07e-1578
epithelial tube1.17e-13117
splanchnic layer of lateral plate mesoderm1.10e-1183
vessel2.61e-1168
epithelial tube open at both ends3.91e-1059
blood vessel3.91e-1059
blood vasculature3.91e-1059
vascular cord3.91e-1059
artery4.89e-1042
arterial blood vessel4.89e-1042
arterial system4.89e-1042
cardiovascular system4.09e-09109
circulatory system1.19e-08112
cell layer1.83e-08309
multi-cellular organism3.93e-08656
epithelium4.43e-08306
systemic artery4.63e-0833
systemic arterial system4.63e-0833
surface structure9.90e-0899
multi-tissue structure1.65e-07342
anatomical system1.94e-07624
anatomical group3.04e-07625
mesoderm7.43e-07315
mesoderm-derived structure7.43e-07315
presumptive mesoderm7.43e-07315
integument8.09e-0746
integumental system8.09e-0746


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
CCNT2#90536.336201576962630.003930750035764890.0189294786270692
CEBPB#105137.971147625824820.001974187055288560.0114979992118716
E2F1#186934.907389214879320.008460985347239390.0323861773384766
E2F4#1874312.66806031528440.0004917987006298980.0043583338561804
E2F6#187635.017155731697390.00791769806886330.0320696710728724
EGR1#195834.988179094810140.008056488137383440.0319272810419742
ELF1#199734.258097958807540.01295179875054610.0460327687496438
EP300#203336.77394172622320.003216880500103790.0166973700387824
ETS1#211339.728760922202340.001085840092584840.00760284616716732
FOXA1#3169311.08141974938550.000734755275698670.00579848165624099
HDAC2#3066313.41562023662630.0004140761399857210.00390057707080082
IRF1#365937.63716375356390.002244692747297240.0127687072894867
JUND#372736.994663941871030.002921845042734990.0156241141988736
MAX#414936.452555509007120.003721913834265510.0185871447873024
MXI1#460139.96157162875930.001011470541259020.00718569973869471
NRF1#4899312.21027944771090.0005492172401020010.00469699470512716
PAX5#507936.669565531177830.003370290999677260.0172400363283192
PBX3#5090321.91451268674419.49854535978121e-050.00136191457829515
POU2F2#545239.106124057742520.001324165192682130.00879903852888776
SIN3A#2594235.408884726815140.006318961977991520.0275597623828387
SIX5#147912317.0867153554590.0002004060546325010.00239093076762209
SP1#666735.69838137814090.005403962701712170.0245587424656941
TAF7#6879311.43306940492390.0006690181981945830.0054088552098811
TCF7L2#6934310.77017656313730.0008003181298398380.00612071068851368
USF1#739136.361499277207960.00388404057290560.0189624772528837
YY1#752834.911170749853860.008441455341808260.0328129058524309
ZBTB33#10009331.66472502998123.14815888737575e-050.00063314185641948
ZBTB7A#5134137.35190930787590.002516255860282270.013969553784394
ZEB1#6935316.88843201754390.0002075486917327580.0024213782189318



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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