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Coexpression cluster:C3782: Difference between revisions

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|full_id=C3782_small_papillotubular_smallcell_Intestinal_immature_bile_colon
|full_id=C3782_small_papillotubular_smallcell_Intestinal_immature_bile_colon
|id=C3782
|id=C3782
|ontology_enrichment_celltype=CL:0000066!2.17e-21!254;CL:0002076!2.81e-11!43;CL:0000223!7.84e-10!59;CL:1000497!1.70e-08!18;CL:0002518!1.70e-08!18;CL:1000507!2.37e-08!12;CL:1000494!2.37e-08!12;CL:0002251!8.19e-08!21;CL:1000449!6.60e-07!16
|ontology_enrichment_celltype=CL:0000066!1.08e-13!253;CL:0002076!2.45e-11!42;CL:0000223!1.42e-09!58;CL:0002251!2.83e-08!20;CL:1000507!1.17e-07!10;CL:1000494!1.17e-07!10;CL:0000082!4.78e-07!19
|ontology_enrichment_disease=DOID:305!2.89e-19!106;DOID:299!1.84e-12!25;DOID:0050687!2.12e-11!143;DOID:0050615!2.33e-07!16;DOID:1749!6.74e-07!14;DOID:162!6.84e-07!235
|ontology_enrichment_disease=DOID:305!9.49e-22!106;DOID:299!1.09e-14!25;DOID:0050687!9.54e-13!143;DOID:0050615!6.40e-09!16;DOID:162!3.07e-08!235;DOID:14566!8.55e-08!239;DOID:1324!1.24e-07!15
|ontology_enrichment_uberon=UBERON:0004119!6.37e-19!169;UBERON:0000925!6.37e-19!169;UBERON:0006595!6.37e-19!169;UBERON:0001007!1.60e-18!155;UBERON:0001555!1.60e-18!155;UBERON:0007026!1.60e-18!155;UBERON:0004921!5.86e-16!129;UBERON:0004185!5.86e-16!129;UBERON:0000464!1.29e-15!104;UBERON:0000466!3.34e-15!126;UBERON:0005177!2.54e-14!107;UBERON:0000077!3.72e-12!130;UBERON:0000058!7.45e-12!26;UBERON:0005409!9.62e-12!35;UBERON:0005911!3.20e-11!82;UBERON:0002553!1.42e-10!70;UBERON:0000160!2.88e-10!27;UBERON:0006554!1.09e-09!44;UBERON:0001008!2.68e-09!45;UBERON:0003064!2.93e-09!37;UBERON:0009569!3.25e-09!113;UBERON:0005153!3.62e-09!37;UBERON:0001041!3.99e-09!98;UBERON:0001004!5.33e-09!72;UBERON:0003886!1.45e-08!63;UBERON:0009773!2.37e-08!12;UBERON:0001231!2.37e-08!12;UBERON:0004810!2.37e-08!12;UBERON:0002113!2.57e-08!27;UBERON:0003918!2.57e-08!27;UBERON:0005095!2.57e-08!27;UBERON:0007687!2.57e-08!27;UBERON:0002108!4.12e-08!14;UBERON:0000080!4.35e-08!18;UBERON:0002120!4.35e-08!18;UBERON:0004875!4.35e-08!18;UBERON:0005721!4.35e-08!18;UBERON:0005754!4.35e-08!18;UBERON:0007297!4.35e-08!18;UBERON:0000489!5.53e-08!32;UBERON:0002048!6.14e-08!22;UBERON:0000117!6.14e-08!22;UBERON:0000171!6.14e-08!22;UBERON:0000170!6.14e-08!22;UBERON:0005597!6.14e-08!22;UBERON:0000118!6.14e-08!22;UBERON:0002075!8.85e-08!18;UBERON:0006555!1.54e-07!17;UBERON:0005103!1.54e-07!17;UBERON:0000083!1.54e-07!17;UBERON:0009201!1.54e-07!17;UBERON:0004819!1.54e-07!17;UBERON:0006553!1.54e-07!17;UBERON:0003074!1.54e-07!17;UBERON:0003060!1.54e-07!17;UBERON:0003887!2.75e-07!21;UBERON:0005172!2.78e-07!55;UBERON:0005173!2.78e-07!55;UBERON:0000344!3.20e-07!12;UBERON:0000481!3.31e-07!347;UBERON:0004211!6.60e-07!16;UBERON:0001285!6.60e-07!16;UBERON:0007684!6.60e-07!16;UBERON:0003220!6.60e-07!16;UBERON:0004208!6.60e-07!16;UBERON:0004876!6.74e-07!20;UBERON:0003104!7.26e-07!238;UBERON:0009142!7.26e-07!238;UBERON:0002294!8.20e-07!7;UBERON:0001173!8.20e-07!7;UBERON:0004912!8.20e-07!7
|ontology_enrichment_uberon=UBERON:0001007!4.81e-20!145;UBERON:0001555!4.81e-20!145;UBERON:0007026!4.81e-20!145;UBERON:0004119!1.30e-17!160;UBERON:0000925!1.30e-17!160;UBERON:0006595!1.30e-17!160;UBERON:0004921!1.99e-16!118;UBERON:0005911!9.60e-15!82;UBERON:0005177!5.03e-14!101;UBERON:0000466!1.69e-11!117;UBERON:0000464!2.76e-11!95;UBERON:0002048!1.70e-10!22;UBERON:0000117!1.70e-10!22;UBERON:0000171!1.70e-10!22;UBERON:0000170!1.70e-10!22;UBERON:0005597!1.70e-10!22;UBERON:0000118!1.70e-10!22;UBERON:0005153!1.70e-10!37;UBERON:0001004!4.72e-10!74;UBERON:0005409!7.40e-10!25;UBERON:0000160!2.62e-09!17;UBERON:0009569!2.79e-09!112;UBERON:0000475!2.85e-09!264;UBERON:0001041!9.77e-09!87;UBERON:0004807!3.21e-08!28;UBERON:0005178!6.44e-08!34;UBERON:0002224!6.44e-08!34;UBERON:0000344!1.00e-07!20;UBERON:0004810!1.17e-07!10;UBERON:0005181!1.38e-07!35;UBERON:0003929!1.55e-07!54;UBERON:0002294!2.34e-07!9;UBERON:0001173!2.34e-07!9;UBERON:0004912!2.34e-07!9;UBERON:0003350!2.55e-07!8;UBERON:0005157!2.78e-07!47;UBERON:0000481!2.78e-07!342;UBERON:0006555!4.32e-07!16;UBERON:0004819!4.32e-07!16;UBERON:0004802!4.78e-07!19;UBERON:0000115!4.78e-07!19;UBERON:0002108!4.94e-07!4;UBERON:0002113!8.87e-07!26;UBERON:0003918!8.87e-07!26;UBERON:0011143!8.87e-07!26;UBERON:0005095!8.87e-07!26;UBERON:0007687!8.87e-07!26
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325328344260487!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00914977727610823!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462199449773896!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167439712210486!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000676166441822196!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00581165603140664!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00391257558888706!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156746750779844!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186459902593589!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294430573805712!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269570076138259!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308983740578835!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172874525669316!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.0088203640894527!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276660547505432!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109058505166875!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00542818455572126!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00629262307590023!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190229466044686!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242707175186177
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}}
}}

Revision as of 15:24, 19 October 2012


Full id: C3782_small_papillotubular_smallcell_Intestinal_immature_bile_colon



Phase1 CAGE Peaks

Hg19::chr19:38423243..38423265,+p4@SIPA1L3
Hg19::chr19:38423275..38423287,+p8@SIPA1L3
Hg19::chr19:38423290..38423301,+p10@SIPA1L3


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>

Cell Type
Ontology termp-valuen
epithelial cell1.08e-13253
endo-epithelial cell2.45e-1142
endodermal cell1.42e-0958
epithelial cell of alimentary canal2.83e-0820
kidney tubule cell1.17e-0710
nephron tubule epithelial cell1.17e-0710
epithelial cell of lung4.78e-0719
Uber Anatomy
Ontology termp-valuen
digestive system4.81e-20145
digestive tract4.81e-20145
primitive gut4.81e-20145
endoderm-derived structure1.30e-17160
endoderm1.30e-17160
presumptive endoderm1.30e-17160
subdivision of digestive tract1.99e-16118
endo-epithelium9.60e-1582
trunk region element5.03e-14101
immaterial anatomical entity1.69e-11117
anatomical space2.76e-1195
lung1.70e-1022
respiratory tube1.70e-1022
respiration organ1.70e-1022
pair of lungs1.70e-1022
lung primordium1.70e-1022
lung bud1.70e-1022
epithelial bud1.70e-1037
respiratory system4.72e-1074
gastrointestinal system7.40e-1025
intestine2.62e-0917
subdivision of trunk2.79e-09112
organism subdivision2.85e-09264
foregut9.77e-0987
respiratory system epithelium3.21e-0828
thoracic cavity element6.44e-0834
thoracic cavity6.44e-0834
mucosa1.00e-0720
nephron tubule epithelium1.17e-0710
thoracic segment organ1.38e-0735
gut epithelium1.55e-0754
biliary system2.34e-079
biliary tree2.34e-079
biliary bud2.34e-079
epithelium of mucosa2.55e-078
epithelial fold2.78e-0747
multi-tissue structure2.78e-07342
excretory tube4.32e-0716
kidney epithelium4.32e-0716
respiratory tract epithelium4.78e-0719
lung epithelium4.78e-0719
small intestine4.94e-074
kidney8.87e-0726
kidney mesenchyme8.87e-0726
upper urinary tract8.87e-0726
kidney rudiment8.87e-0726
kidney field8.87e-0726
Disease
Ontology termp-valuen
carcinoma9.49e-22106
adenocarcinoma1.09e-1425
cell type cancer9.54e-13143
respiratory system cancer6.40e-0916
cancer3.07e-08235
disease of cellular proliferation8.55e-08239
lung cancer1.24e-0715


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
E2F1#186934.907389214879320.008460985347239390.0325328344260487
EBF1#187938.9064668465690.00141523283560980.00914977727610823
ELF1#199734.258097958807540.01295179875054610.0462199449773896
EP300#203336.77394172622320.003216880500103790.0167439712210486
ESR1#2099330.76860329615453.43136389821584e-050.000676166441822196
FOXA1#3169311.08141974938550.000734755275698670.00581165603140664
HDAC2#3066313.41562023662630.0004140761399857210.00391257558888706
JUND#372736.994663941871030.002921845042734990.0156746750779844
MAX#414936.452555509007120.003721913834265510.0186459902593589
MYC#460935.22228187160940.007020843755740150.0294430573805712
NFKB1#479035.488063424193840.006049381815655430.0269570076138259
NR3C1#2908314.9730233311730.0002978331194675480.00308983740578835
PAX5#507936.669565531177830.003370290999677260.0172874525669316
POU2F2#545239.106124057742520.001324165192682130.0088203640894527
SIN3A#2594235.408884726815140.006318961977991520.0276660547505432
SPI1#668838.204323508522730.001810593189410520.0109058505166875
TAF7#6879311.43306940492390.0006690181981945830.00542818455572126
TCF12#6938310.63446490218640.0008313523990202070.00629262307590023
USF1#739136.361499277207960.00388404057290560.0190229466044686
ZEB1#6935316.88843201754390.0002075486917327580.00242707175186177



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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