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Coexpression cluster:C4495: Difference between revisions

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|full_id=C4495_Endothelial_Lymphatic_Mast_gall_Iris_osteosarcoma_Lens
|full_id=C4495_Endothelial_Lymphatic_Mast_gall_Iris_osteosarcoma_Lens
|id=C4495
|id=C4495
|ontology_enrichment_celltype=CL:0000222!8.00e-28!119;CL:0000055!2.68e-25!180;CL:0002321!5.96e-19!248;CL:0000220!6.18e-19!246;CL:0002139!2.48e-17!24;CL:0000115!2.21e-14!35;CL:0000213!5.36e-14!57;CL:0000215!5.36e-14!57;CL:0000057!1.23e-13!75;CL:0000680!1.68e-13!57;CL:0000056!1.68e-13!57;CL:0000355!1.68e-13!57;CL:0000071!2.43e-13!18;CL:0002546!2.43e-13!18;CL:0000187!9.46e-13!54;CL:0002078!2.11e-12!44;CL:0000183!1.26e-11!59;CL:0000192!1.56e-11!42;CL:0000514!1.56e-11!42;CL:0000359!1.96e-11!32;CL:0000393!2.15e-11!60;CL:0000211!2.15e-11!60;CL:1000413!2.17e-07!9;CL:0002620!5.98e-07!23
|ontology_enrichment_celltype=CL:0000222!3.12e-21!121;CL:0002139!2.37e-20!24;CL:0000115!2.86e-16!36;CL:0000071!1.04e-15!18;CL:0002546!1.04e-15!18;CL:0000057!1.21e-14!76;CL:0002078!3.29e-13!45;CL:0000213!1.87e-12!58;CL:0000215!1.87e-12!58;CL:0002321!3.03e-11!250;CL:0000680!5.63e-09!58;CL:0000056!5.63e-09!58;CL:0000355!5.63e-09!58;CL:0000359!9.66e-09!32;CL:1000413!1.55e-08!9;CL:0000187!1.72e-08!55;CL:0002620!5.41e-08!23;CL:0000192!1.13e-07!43;CL:0000514!1.13e-07!43;CL:0000393!1.78e-07!61;CL:0000211!1.78e-07!61;CL:0000183!1.80e-07!59
|ontology_enrichment_disease=DOID:2394!8.73e-08!14
|ontology_enrichment_disease=DOID:2394!1.27e-07!14
|ontology_enrichment_uberon=UBERON:0002049!6.69e-32!79;UBERON:0007798!6.69e-32!79;UBERON:0004872!6.56e-28!84;UBERON:0000055!3.71e-27!69;UBERON:0001981!4.92e-25!60;UBERON:0007500!4.92e-25!60;UBERON:0004537!4.92e-25!60;UBERON:0006965!4.92e-25!60;UBERON:0004535!2.93e-23!110;UBERON:0001009!3.57e-22!113;UBERON:0003914!8.87e-22!118;UBERON:0000490!1.35e-18!138;UBERON:0001637!1.26e-16!42;UBERON:0003509!1.26e-16!42;UBERON:0004572!1.26e-16!42;UBERON:0000914!1.32e-16!83;UBERON:0002329!1.32e-16!83;UBERON:0003077!1.32e-16!83;UBERON:0003059!1.32e-16!83;UBERON:0007282!1.32e-16!83;UBERON:0009618!1.32e-16!83;UBERON:0007285!1.32e-16!83;UBERON:0000468!1.69e-15!659;UBERON:0000467!3.70e-15!625;UBERON:0000480!7.77e-15!626;UBERON:0005256!1.73e-14!143;UBERON:0004290!2.32e-14!70;UBERON:0000486!1.50e-13!82;UBERON:0000477!1.63e-13!286;UBERON:0001986!2.43e-13!18;UBERON:0004638!2.43e-13!18;UBERON:0004852!2.43e-13!18;UBERON:0000119!2.44e-13!312;UBERON:0004573!4.71e-13!33;UBERON:0004571!4.71e-13!33;UBERON:0001134!9.26e-13!61;UBERON:0002036!9.26e-13!61;UBERON:0003082!9.26e-13!61;UBERON:0002385!1.23e-12!63;UBERON:0001015!1.23e-12!63;UBERON:0000383!1.23e-12!63;UBERON:0000483!1.54e-12!309;UBERON:0000487!2.05e-12!22;UBERON:0004111!1.99e-11!241;UBERON:0006914!4.15e-11!25;UBERON:0002100!5.75e-11!216;UBERON:0000947!6.10e-10!21;UBERON:0010191!6.10e-10!21;UBERON:0000475!3.47e-09!365;UBERON:0000926!6.79e-09!448;UBERON:0004120!6.79e-09!448;UBERON:0006603!6.79e-09!448;UBERON:0000481!1.44e-08!347;UBERON:0000025!2.17e-08!194;UBERON:0003104!2.26e-08!238;UBERON:0009142!2.26e-08!238;UBERON:0002050!2.40e-08!605;UBERON:0005423!2.40e-08!605;UBERON:0000922!3.23e-08!612;UBERON:0000923!4.21e-08!604;UBERON:0005291!4.21e-08!604;UBERON:0006598!4.21e-08!604;UBERON:0002532!4.21e-08!604;UBERON:0003915!2.17e-07!9;UBERON:0004700!2.17e-07!9;UBERON:0001917!2.17e-07!9;UBERON:0001638!9.95e-07!9;UBERON:0003920!9.95e-07!9;UBERON:0004582!9.95e-07!9
|ontology_enrichment_uberon=UBERON:0002049!7.96e-29!78;UBERON:0007798!7.96e-29!78;UBERON:0000055!8.27e-24!68;UBERON:0004872!2.07e-22!83;UBERON:0004535!4.86e-22!109;UBERON:0007500!7.98e-22!59;UBERON:0001981!7.98e-22!59;UBERON:0004537!7.98e-22!59;UBERON:0006965!7.98e-22!59;UBERON:0001009!1.37e-21!112;UBERON:0003914!2.71e-18!117;UBERON:0004638!1.04e-15!18;UBERON:0001986!1.04e-15!18;UBERON:0004852!1.04e-15!18;UBERON:0001637!1.41e-14!42;UBERON:0003509!1.41e-14!42;UBERON:0004572!1.41e-14!42;UBERON:0000490!2.61e-13!148;UBERON:0000487!5.95e-13!22;UBERON:0006914!1.30e-11!25;UBERON:0004573!1.47e-10!33;UBERON:0004571!1.47e-10!33;UBERON:0007503!2.00e-10!78;UBERON:0002329!2.06e-09!71;UBERON:0003059!2.06e-09!71;UBERON:0007282!2.06e-09!71;UBERON:0004290!2.06e-09!71;UBERON:0009618!2.06e-09!71;UBERON:0007524!3.36e-09!73;UBERON:0000486!4.55e-09!83;UBERON:0003077!4.78e-09!72;UBERON:0007285!4.78e-09!72;UBERON:0000119!7.84e-09!309;UBERON:0000947!1.09e-08!21;UBERON:0010191!1.09e-08!21;UBERON:0004111!1.23e-08!240;UBERON:0003915!1.55e-08!9;UBERON:0004700!1.55e-08!9;UBERON:0001917!1.55e-08!9;UBERON:0002385!2.66e-08!64;UBERON:0001015!2.66e-08!64;UBERON:0000383!2.66e-08!64;UBERON:0000477!3.68e-08!373;UBERON:0000483!4.40e-08!306;UBERON:0000468!5.14e-08!656;UBERON:0001134!5.27e-08!62;UBERON:0002036!5.27e-08!62;UBERON:0003082!5.27e-08!62;UBERON:0000467!5.57e-08!624;UBERON:0000480!7.56e-08!625;UBERON:0000926!8.88e-08!315;UBERON:0004120!8.88e-08!315;UBERON:0006603!8.88e-08!315;UBERON:0001638!1.74e-07!9;UBERON:0003920!1.74e-07!9;UBERON:0004582!1.74e-07!9;UBERON:0000025!7.09e-07!192
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.019086131525652!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280914397982324!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327134921027815!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00438512460472005!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032388722283264!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322071412279498!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464421104754612!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00900788358649988!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154679430671846!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438486519958007!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109055159776444!MAX#4149;3:6.45255550900712:0.00372191383426551:0.018723229080336!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295665282663607!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000740013192592598!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00667374405372622!REST#5978;3:9.65002871612802:0.00111263624711459:0.00770370041185366!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277930541174755!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00545020215298316!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190963804441055!USF2#7392;3:12.9921973850696:0.000455897939342781:0.004226302581841!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330862851626178!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140750493166954
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}}
}}

Revision as of 15:59, 19 October 2012


Full id: C4495_Endothelial_Lymphatic_Mast_gall_Iris_osteosarcoma_Lens



Phase1 CAGE Peaks

Hg19::chr5:34656529..34656549,+p3@RAI14
Hg19::chr5:34656551..34656562,+p8@RAI14
Hg19::chr5:34656634..34656645,+p15@RAI14


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
vasculature7.96e-2978
vascular system7.96e-2978
vessel8.27e-2468
splanchnic layer of lateral plate mesoderm2.07e-2283
cardiovascular system4.86e-22109
epithelial tube open at both ends7.98e-2259
blood vessel7.98e-2259
blood vasculature7.98e-2259
vascular cord7.98e-2259
circulatory system1.37e-21112
epithelial tube2.71e-18117
blood vessel endothelium1.04e-1518
endothelium1.04e-1518
cardiovascular system endothelium1.04e-1518
artery1.41e-1442
arterial blood vessel1.41e-1442
arterial system1.41e-1442
unilaminar epithelium2.61e-13148
simple squamous epithelium5.95e-1322
squamous epithelium1.30e-1125
systemic artery1.47e-1033
systemic arterial system1.47e-1033
epithelial vesicle2.00e-1078
somite2.06e-0971
presomitic mesoderm2.06e-0971
presumptive segmental plate2.06e-0971
dermomyotome2.06e-0971
trunk paraxial mesoderm2.06e-0971
dense mesenchyme tissue3.36e-0973
multilaminar epithelium4.55e-0983
paraxial mesoderm4.78e-0972
presumptive paraxial mesoderm4.78e-0972
cell layer7.84e-09309
aorta1.09e-0821
aortic system1.09e-0821
anatomical conduit1.23e-08240
endothelial tube1.55e-089
arterial system endothelium1.55e-089
endothelium of artery1.55e-089
muscle tissue2.66e-0864
musculature2.66e-0864
musculature of body2.66e-0864
anatomical cluster3.68e-08373
epithelium4.40e-08306
multi-cellular organism5.14e-08656
skeletal muscle tissue5.27e-0862
striated muscle tissue5.27e-0862
myotome5.27e-0862
anatomical system5.57e-08624
anatomical group7.56e-08625
mesoderm8.88e-08315
mesoderm-derived structure8.88e-08315
presumptive mesoderm8.88e-08315
vein1.74e-079
venous blood vessel1.74e-079
venous system1.74e-079
tube7.09e-07192
Disease
Ontology termp-valuen
ovarian cancer1.27e-0714


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#90536.336201576962630.003930750035764890.019086131525652
CTCF#1066435.360256373075030.0064925092527670.0280914397982324
E2F1#186934.907389214879320.008460985347239390.0327134921027815
E2F4#1874312.66806031528440.0004917987006298980.00438512460472005
E2F6#187635.017155731697390.00791769806886330.032388722283264
EGR1#195834.988179094810140.008056488137383440.0322071412279498
ELF1#199734.258097958807540.01295179875054610.0464421104754612
FOS#235338.99795530889440.001372499272417130.00900788358649988
GABPB1#255337.067683836182170.002832212825417420.0154679430671846
GATA2#2624312.7449317335540.0004829527704283790.00438486519958007
HMGN3#932438.178547723350590.001827766942164210.0109055159776444
MAX#414936.452555509007120.003721913834265510.018723229080336
MYC#460935.22228187160940.007020843755740150.0295665282663607
NANOG#79923329.24477848101273.99627955670032e-050.000740013192592598
RAD21#5885310.35503389545630.0009004912073565420.00667374405372622
REST#597839.650028716128020.001112636247114590.00770370041185366
SIN3A#2594235.408884726815140.006318961977991520.0277930541174755
TAF7#6879311.43306940492390.0006690181981945830.00545020215298316
USF1#739136.361499277207960.00388404057290560.0190963804441055
USF2#7392312.99219738506960.0004558979393427810.004226302581841
YY1#752834.911170749853860.008441455341808260.0330862851626178
ZBTB7A#5134137.35190930787590.002516255860282270.0140750493166954



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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