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Coexpression cluster:C2933: Difference between revisions

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|full_id=C2933_testicular_rectal_squamous_malignant_nasal_small_large
|full_id=C2933_testicular_rectal_squamous_malignant_nasal_small_large
|id=C2933
|id=C2933
|ontology_enrichment_celltype=CL:0000066!9.45e-30!254;CL:0002076!2.33e-20!43;CL:0000223!1.67e-15!59;CL:0002251!3.20e-10!21;CL:0002368!9.91e-10!13;CL:0002159!7.86e-09!13;CL:0000039!2.81e-08!7;CL:0000586!2.81e-08!7;CL:0000082!3.67e-08!19
|ontology_enrichment_celltype=CL:0000066!1.38e-32!253;CL:0002076!1.22e-23!42;CL:0000223!1.96e-17!58;CL:0002251!3.42e-12!20;CL:0002368!1.42e-10!13;CL:0000039!4.47e-09!7;CL:0000586!4.47e-09!7;CL:0002159!6.01e-09!14;CL:0000082!2.77e-08!19
|ontology_enrichment_disease=DOID:305!2.76e-24!106;DOID:0050687!2.52e-16!143;DOID:1749!1.01e-13!14;DOID:299!3.47e-07!25
|ontology_enrichment_disease=DOID:305!7.59e-26!106;DOID:0050687!3.00e-18!143;DOID:1749!4.75e-15!14;DOID:299!2.93e-08!25
|ontology_enrichment_uberon=UBERON:0004119!7.52e-24!169;UBERON:0000925!7.52e-24!169;UBERON:0006595!7.52e-24!169;UBERON:0001007!7.86e-18!155;UBERON:0001555!7.86e-18!155;UBERON:0007026!7.86e-18!155;UBERON:0001004!5.02e-16!72;UBERON:0000464!1.03e-15!104;UBERON:0004921!1.89e-15!129;UBERON:0004185!1.89e-15!129;UBERON:0000077!7.37e-15!130;UBERON:0000466!1.18e-13!126;UBERON:0005153!1.22e-13!37;UBERON:0005911!2.46e-12!82;UBERON:0005181!4.17e-11!35;UBERON:0005157!5.71e-11!51;UBERON:0000065!6.60e-11!53;UBERON:0005178!8.76e-11!34;UBERON:0002224!8.76e-11!34;UBERON:0000161!1.15e-10!35;UBERON:0002048!1.09e-09!22;UBERON:0000117!1.09e-09!22;UBERON:0000171!1.09e-09!22;UBERON:0000170!1.09e-09!22;UBERON:0005597!1.09e-09!22;UBERON:0000118!1.09e-09!22;UBERON:0005156!1.85e-09!59;UBERON:0000990!1.85e-09!59;UBERON:0001041!5.61e-09!98;UBERON:0000915!8.89e-09!52;UBERON:0004807!2.28e-08!28;UBERON:0004802!3.67e-08!19;UBERON:0000115!3.67e-08!19;UBERON:0003101!4.91e-08!22;UBERON:0000079!4.91e-08!22;UBERON:0003133!9.71e-08!48;UBERON:0000166!1.05e-07!21;UBERON:0008947!1.38e-07!38;UBERON:0003258!1.38e-07!38;UBERON:0000344!1.65e-07!12;UBERON:0005631!3.31e-07!14;UBERON:0000158!3.31e-07!14;UBERON:0000072!3.49e-07!46;UBERON:0002553!4.15e-07!70;UBERON:0005177!4.32e-07!107;UBERON:0003135!6.08e-07!11;UBERON:0000062!6.54e-07!511
|ontology_enrichment_uberon=UBERON:0004119!2.82e-25!160;UBERON:0000925!2.82e-25!160;UBERON:0006595!2.82e-25!160;UBERON:0001007!7.82e-19!145;UBERON:0001555!7.82e-19!145;UBERON:0007026!7.82e-19!145;UBERON:0004921!1.55e-16!118;UBERON:0001004!1.56e-15!74;UBERON:0005153!1.02e-13!37;UBERON:0000464!1.37e-13!95;UBERON:0005911!1.44e-12!82;UBERON:0005178!2.12e-11!34;UBERON:0002224!2.12e-11!34;UBERON:0000466!3.97e-11!117;UBERON:0005157!6.20e-11!47;UBERON:0005181!7.32e-11!35;UBERON:0000065!7.52e-11!54;UBERON:0000161!8.47e-11!36;UBERON:0005156!3.78e-10!59;UBERON:0000990!3.78e-10!59;UBERON:0002048!5.69e-10!22;UBERON:0000117!5.69e-10!22;UBERON:0000171!5.69e-10!22;UBERON:0000170!5.69e-10!22;UBERON:0005597!5.69e-10!22;UBERON:0000118!5.69e-10!22;UBERON:0001041!1.55e-09!87;UBERON:0000915!4.85e-09!52;UBERON:0004807!7.24e-09!28;UBERON:0003133!1.18e-08!48;UBERON:0004802!2.77e-08!19;UBERON:0000115!2.77e-08!19;UBERON:0000166!4.58e-08!22;UBERON:0003101!1.46e-07!22;UBERON:0000079!1.46e-07!22;UBERON:0008947!1.91e-07!38;UBERON:0003258!1.91e-07!38;UBERON:0001008!2.40e-07!48;UBERON:0005177!3.35e-07!101;UBERON:0006554!5.05e-07!47;UBERON:0005631!5.79e-07!14;UBERON:0000158!5.79e-07!14;UBERON:0000072!6.28e-07!47;UBERON:0004175!6.74e-07!25;UBERON:0000344!7.07e-07!20;UBERON:0003135!9.39e-07!11
|tf_chipseq_enrich=ATF3#467;4:22.4631745260087:3.92475754624726e-06:0.000127654236490974!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00820516427824846!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00435671084328954!GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.80132832047766e-05!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.00062897806986736!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392854124862704!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486837270298245!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00890230986829556!NANOG#79923;4:29.2447784810127:1.36586687657858e-06:5.35271184701653e-05!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00798499611918456!SP1#6667;4:5.6983813781409:0.000948260606533398:0.0068607820911494!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323519438305023!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245179026904066!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00120331257693967!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115865291735055!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00509388260377782!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000683594231466611!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107132932824065!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.000305441944874063
|tf_chipseq_enrich=ATF3#467;4:22.4631745260087:3.92475754624726e-06:0.000127654236490974!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00820516427824846!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00435671084328954!GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.80132832047766e-05!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.00062897806986736!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392854124862704!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486837270298245!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00890230986829556!NANOG#79923;4:29.2447784810127:1.36586687657858e-06:5.35271184701653e-05!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00798499611918456!SP1#6667;4:5.6983813781409:0.000948260606533398:0.0068607820911494!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323519438305023!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245179026904066!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00120331257693967!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115865291735055!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00509388260377782!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000683594231466611!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107132932824065!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.000305441944874063
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}}
}}

Revision as of 14:35, 19 October 2012


Full id: C2933_testicular_rectal_squamous_malignant_nasal_small_large



Phase1 CAGE Peaks

Hg19::chr8:95653327..95653364,+p3@ESRP1
Hg19::chr8:95653373..95653415,+p1@ESRP1
Hg19::chr8:95653432..95653460,+p2@ESRP1
Hg19::chr8:95653478..95653491,+p4@ESRP1


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
endoderm-derived structure2.82e-25160
endoderm2.82e-25160
presumptive endoderm2.82e-25160
digestive system7.82e-19145
digestive tract7.82e-19145
primitive gut7.82e-19145
subdivision of digestive tract1.55e-16118
respiratory system1.56e-1574
epithelial bud1.02e-1337
anatomical space1.37e-1395
endo-epithelium1.44e-1282
thoracic cavity element2.12e-1134
thoracic cavity2.12e-1134
immaterial anatomical entity3.97e-11117
epithelial fold6.20e-1147
thoracic segment organ7.32e-1135
respiratory tract7.52e-1154
orifice8.47e-1136
reproductive structure3.78e-1059
reproductive system3.78e-1059
lung5.69e-1022
respiratory tube5.69e-1022
respiration organ5.69e-1022
pair of lungs5.69e-1022
lung primordium5.69e-1022
lung bud5.69e-1022
foregut1.55e-0987
thoracic segment of trunk4.85e-0952
respiratory system epithelium7.24e-0928
reproductive organ1.18e-0848
respiratory tract epithelium2.77e-0819
lung epithelium2.77e-0819
oral opening4.58e-0822
male organism1.46e-0722
male reproductive system1.46e-0722
respiratory primordium1.91e-0738
endoderm of foregut1.91e-0738
renal system2.40e-0748
trunk region element3.35e-07101
urinary system structure5.05e-0747
extraembryonic membrane5.79e-0714
membranous layer5.79e-0714
segment of respiratory tract6.28e-0747
internal genitalia6.74e-0725
mucosa7.07e-0720
male reproductive organ9.39e-0711
Disease
Ontology termp-valuen
carcinoma7.59e-26106
cell type cancer3.00e-18143
squamous cell carcinoma4.75e-1514
adenocarcinoma2.93e-0825


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
ATF3#467422.46317452600873.92475754624726e-060.000127654236490974
CTCF#1066445.360256373075030.001211145381643620.00820516427824846
EP300#203346.77394172622320.0004748459821442640.00435671084328954
GATA3#2625427.2365163572061.81561517799785e-066.80132832047766e-05
HDAC2#3066413.41562023662633.0859005065161e-050.00062897806986736
JUND#372746.994663941871030.000417684217818580.00392854124862704
MAX#414946.452555509007120.0005767613195645490.00486837270298245
MYC#460945.22228187160940.001344309395272740.00890230986829556
NANOG#79923429.24477848101271.36586687657858e-065.35271184701653e-05
SIN3A#2594245.408884726815140.001168172384885160.00798499611918456
SP1#666745.69838137814090.0009482606065333980.0068607820911494
TAF1#687243.343046285745290.008005664898701650.0323519438305023
TBP#690843.706770687096390.005296377814784350.0245179026904066
TCF12#6938410.63446490218647.8163066689251e-050.00120331257693967
TCF7L2#6934410.77017656313737.42969445082454e-050.00115865291735055
USF1#739146.361499277207960.0006105011399140830.00509388260377782
USF2#7392412.99219738506963.50833029870167e-050.000683594231466611
YY1#752844.911170749853860.00171871838055440.0107132932824065
ZEB1#6935416.88843201754391.22862303393937e-050.000305441944874063



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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