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|ontology_enrichment_disease=DOID:305!2.82e-08!106;DOID:1749!4.56e-07!14
|ontology_enrichment_disease=DOID:305!2.82e-08!106;DOID:1749!4.56e-07!14
|ontology_enrichment_uberon=UBERON:0000481!4.12e-20!347;UBERON:0003104!9.97e-19!238;UBERON:0009142!9.97e-19!238;UBERON:0005256!1.82e-15!143;UBERON:0000486!4.59e-14!82;UBERON:0000477!4.67e-14!286;UBERON:0002100!6.53e-14!216;UBERON:0000119!1.04e-13!312;UBERON:0003914!1.34e-13!118;UBERON:0000914!1.57e-13!83;UBERON:0002329!1.57e-13!83;UBERON:0003077!1.57e-13!83;UBERON:0003059!1.57e-13!83;UBERON:0007282!1.57e-13!83;UBERON:0009618!1.57e-13!83;UBERON:0007285!1.57e-13!83;UBERON:0000483!3.46e-13!309;UBERON:0000490!6.61e-13!138;UBERON:0000475!1.11e-12!365;UBERON:0002049!2.39e-12!79;UBERON:0007798!2.39e-12!79;UBERON:0001637!2.41e-12!42;UBERON:0003509!2.41e-12!42;UBERON:0004572!2.41e-12!42;UBERON:0004119!2.46e-12!169;UBERON:0000925!2.46e-12!169;UBERON:0006595!2.46e-12!169;UBERON:0001134!3.36e-12!61;UBERON:0002036!3.36e-12!61;UBERON:0003082!3.36e-12!61;UBERON:0002385!1.04e-11!63;UBERON:0001015!1.04e-11!63;UBERON:0000383!1.04e-11!63;UBERON:0001048!1.06e-11!168;UBERON:0004290!5.10e-11!70;UBERON:0001007!6.77e-11!155;UBERON:0001555!6.77e-11!155;UBERON:0007026!6.77e-11!155;UBERON:0000055!9.15e-11!69;UBERON:0001981!9.34e-11!60;UBERON:0007500!9.34e-11!60;UBERON:0004537!9.34e-11!60;UBERON:0006965!9.34e-11!60;UBERON:0004573!9.46e-11!33;UBERON:0004571!9.46e-11!33;UBERON:0004872!1.60e-10!84;UBERON:0001004!2.26e-10!72;UBERON:0000467!3.11e-09!625;UBERON:0000480!5.05e-09!626;UBERON:0004111!6.10e-09!241;UBERON:0000065!1.85e-08!53;UBERON:0000072!1.87e-08!46;UBERON:0000926!2.04e-08!448;UBERON:0004120!2.04e-08!448;UBERON:0006603!2.04e-08!448;UBERON:0000077!3.15e-08!130;UBERON:0004535!3.18e-08!110;UBERON:0001444!3.98e-08!48;UBERON:0000468!5.42e-08!659;UBERON:0001009!6.59e-08!113;UBERON:0003102!1.90e-07!95;UBERON:0000923!2.04e-07!604;UBERON:0005291!2.04e-07!604;UBERON:0006598!2.04e-07!604;UBERON:0002532!2.04e-07!604;UBERON:0002050!2.19e-07!605;UBERON:0005423!2.19e-07!605;UBERON:0001041!2.48e-07!98;UBERON:0008947!2.82e-07!38;UBERON:0003258!2.82e-07!38;UBERON:0005911!4.62e-07!82
|ontology_enrichment_uberon=UBERON:0000481!4.12e-20!347;UBERON:0003104!9.97e-19!238;UBERON:0009142!9.97e-19!238;UBERON:0005256!1.82e-15!143;UBERON:0000486!4.59e-14!82;UBERON:0000477!4.67e-14!286;UBERON:0002100!6.53e-14!216;UBERON:0000119!1.04e-13!312;UBERON:0003914!1.34e-13!118;UBERON:0000914!1.57e-13!83;UBERON:0002329!1.57e-13!83;UBERON:0003077!1.57e-13!83;UBERON:0003059!1.57e-13!83;UBERON:0007282!1.57e-13!83;UBERON:0009618!1.57e-13!83;UBERON:0007285!1.57e-13!83;UBERON:0000483!3.46e-13!309;UBERON:0000490!6.61e-13!138;UBERON:0000475!1.11e-12!365;UBERON:0002049!2.39e-12!79;UBERON:0007798!2.39e-12!79;UBERON:0001637!2.41e-12!42;UBERON:0003509!2.41e-12!42;UBERON:0004572!2.41e-12!42;UBERON:0004119!2.46e-12!169;UBERON:0000925!2.46e-12!169;UBERON:0006595!2.46e-12!169;UBERON:0001134!3.36e-12!61;UBERON:0002036!3.36e-12!61;UBERON:0003082!3.36e-12!61;UBERON:0002385!1.04e-11!63;UBERON:0001015!1.04e-11!63;UBERON:0000383!1.04e-11!63;UBERON:0001048!1.06e-11!168;UBERON:0004290!5.10e-11!70;UBERON:0001007!6.77e-11!155;UBERON:0001555!6.77e-11!155;UBERON:0007026!6.77e-11!155;UBERON:0000055!9.15e-11!69;UBERON:0001981!9.34e-11!60;UBERON:0007500!9.34e-11!60;UBERON:0004537!9.34e-11!60;UBERON:0006965!9.34e-11!60;UBERON:0004573!9.46e-11!33;UBERON:0004571!9.46e-11!33;UBERON:0004872!1.60e-10!84;UBERON:0001004!2.26e-10!72;UBERON:0000467!3.11e-09!625;UBERON:0000480!5.05e-09!626;UBERON:0004111!6.10e-09!241;UBERON:0000065!1.85e-08!53;UBERON:0000072!1.87e-08!46;UBERON:0000926!2.04e-08!448;UBERON:0004120!2.04e-08!448;UBERON:0006603!2.04e-08!448;UBERON:0000077!3.15e-08!130;UBERON:0004535!3.18e-08!110;UBERON:0001444!3.98e-08!48;UBERON:0000468!5.42e-08!659;UBERON:0001009!6.59e-08!113;UBERON:0003102!1.90e-07!95;UBERON:0000923!2.04e-07!604;UBERON:0005291!2.04e-07!604;UBERON:0006598!2.04e-07!604;UBERON:0002532!2.04e-07!604;UBERON:0002050!2.19e-07!605;UBERON:0005423!2.19e-07!605;UBERON:0001041!2.48e-07!98;UBERON:0008947!2.82e-07!38;UBERON:0003258!2.82e-07!38;UBERON:0005911!4.62e-07!82
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}}
}}

Revision as of 12:49, 5 September 2012


Full id: C2343_squamous_malignant_meningioma_embryonic_mesothelioma_bile_papillotubular



Phase1 CAGE Peaks

Hg19::chr15:67418047..67418093,+p4@SMAD3
Hg19::chr15:67418099..67418118,+p16@SMAD3
Hg19::chr15:67418119..67418162,+p5@SMAD3
Hg19::chr15:67418177..67418204,+p9@SMAD3


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
multi-tissue structure4.12e-20347
mesenchyme9.97e-19238
entire embryonic mesenchyme9.97e-19238
trunk mesenchyme1.82e-15143
multilaminar epithelium4.59e-1482
anatomical cluster4.67e-14286
trunk6.53e-14216
cell layer1.04e-13312
epithelial tube1.34e-13118
somite1.57e-1383
paraxial mesoderm1.57e-1383
presomitic mesoderm1.57e-1383
presumptive segmental plate1.57e-1383
trunk paraxial mesoderm1.57e-1383
presumptive paraxial mesoderm1.57e-1383
epithelium3.46e-13309
unilaminar epithelium6.61e-13138
organism subdivision1.11e-12365
vasculature2.39e-1279
vascular system2.39e-1279
artery2.41e-1242
arterial blood vessel2.41e-1242
arterial system2.41e-1242
endoderm-derived structure2.46e-12169
endoderm2.46e-12169
presumptive endoderm2.46e-12169
skeletal muscle tissue3.36e-1261
striated muscle tissue3.36e-1261
myotome3.36e-1261
muscle tissue1.04e-1163
musculature1.04e-1163
musculature of body1.04e-1163
primordium1.06e-11168
dermomyotome5.10e-1170
digestive system6.77e-11155
digestive tract6.77e-11155
primitive gut6.77e-11155
vessel9.15e-1169
blood vessel9.34e-1160
epithelial tube open at both ends9.34e-1160
blood vasculature9.34e-1160
vascular cord9.34e-1160
systemic artery9.46e-1133
systemic arterial system9.46e-1133
splanchnic layer of lateral plate mesoderm1.60e-1084
respiratory system2.26e-1072
anatomical system3.11e-09625
anatomical group5.05e-09626
anatomical conduit6.10e-09241
respiratory tract1.85e-0853
segment of respiratory tract1.87e-0846
mesoderm2.04e-08448
mesoderm-derived structure2.04e-08448
presumptive mesoderm2.04e-08448
mixed endoderm/mesoderm-derived structure3.15e-08130
cardiovascular system3.18e-08110
subdivision of head3.98e-0848
multi-cellular organism5.42e-08659
circulatory system6.59e-08113
surface structure1.90e-0795
germ layer2.04e-07604
embryonic tissue2.04e-07604
presumptive structure2.04e-07604
epiblast (generic)2.04e-07604
embryonic structure2.19e-07605
developing anatomical structure2.19e-07605
foregut2.48e-0798
respiratory primordium2.82e-0738
endoderm of foregut2.82e-0738
endo-epithelium4.62e-0782
Disease
Ontology termp-valuen
carcinoma2.82e-08106
squamous cell carcinoma4.56e-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
BRCA1#672420.18423064322386.02116732184487e-060.000179362434091887
CEBPB#105147.971147625824820.0002476385788090830.00267789661754419
E2F1#186944.907389214879320.001724022357361790.0106403008498114
EP300#203346.77394172622320.0004748459821442640.00433765761647554
ESR1#2099430.76860329615451.11467714392546e-064.59959566315412e-05
FOS#235348.99795530889440.0001525147711168630.00194701016754358
FOSL1#8061439.7135797163734.01511434669553e-071.93688003350824e-05
FOXA1#3169411.08141974938556.62943068949433e-050.00106946418254572
GATA2#2624412.7449317335543.78864877853583e-050.000720996154849679
GATA3#2625427.2365163572061.81561517799785e-066.76251902906266e-05
JUN#3725412.51282919233634.07770316866756e-050.000742065239993851
JUNB#3726430.61063265982111.13787152942193e-064.65120018243825e-05
JUND#372746.994663941871030.000417684217818580.00391198296338935
MAX#414946.452555509007120.0005767613195645490.00485034024108237
MXI1#460149.96157162875930.0001015224754950450.00142206354858194
MYC#460945.22228187160940.001344309395272740.00886800965973278
NR3C1#2908414.9730233311731.98868032687801e-050.000442282335304115
RAD21#5885410.35503389545638.6948481184721e-050.00129190673302761
RFX5#5993412.04791082719514.74457429336527e-050.000826001991373188
SMARCB1#6598418.25271578115749.00423392720929e-060.00024106464678898
SMC3#9126415.04493284493281.95092670935632e-050.000437237842485976
STAT1#6772420.70658749719925.43610708103893e-060.000165137169120601
STAT3#6774410.51946499715428.16377768286615e-050.00123014972936208
TAF1#687243.343046285745290.008005664898701650.0321788721993419
TBP#690843.706770687096390.005296377814784350.0243860337079867
TCF7L2#6934410.77017656313737.42969445082454e-050.00115245783268924
TFAP2A#7020416.5186343730451.34240829060362e-050.000326349579754077
TFAP2C#7022410.80922860986027.32289634782688e-050.00114456146613393
ZBTB7A#5134147.35190930787590.000342223540015990.00346198026886187



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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