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Coexpression cluster:C3782: Difference between revisions

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|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!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_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: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
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}}
}}

Revision as of 12:07, 5 September 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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure6.37e-19169
endoderm6.37e-19169
presumptive endoderm6.37e-19169
digestive system1.60e-18155
digestive tract1.60e-18155
primitive gut1.60e-18155
subdivision of digestive tract5.86e-16129
endodermal part of digestive tract5.86e-16129
anatomical space1.29e-15104
immaterial anatomical entity3.34e-15126
trunk region element2.54e-14107
mixed endoderm/mesoderm-derived structure3.72e-12130
duct7.45e-1226
gastrointestinal system9.62e-1235
endo-epithelium3.20e-1182
anatomical cavity1.42e-1070
intestine2.88e-1027
urinary system structure1.09e-0944
renal system2.68e-0945
intermediate mesoderm2.93e-0937
subdivision of trunk3.25e-09113
epithelial bud3.62e-0937
foregut3.99e-0998
respiratory system5.33e-0972
body cavity precursor1.45e-0863
renal tubule2.37e-0812
nephron tubule2.37e-0812
nephron tubule epithelium2.37e-0812
kidney2.57e-0827
kidney mesenchyme2.57e-0827
kidney rudiment2.57e-0827
kidney field2.57e-0827
small intestine4.12e-0814
mesonephros4.35e-0818
pronephros4.35e-0818
nephrogenic cord4.35e-0818
pronephric mesoderm4.35e-0818
rostral part of nephrogenic cord4.35e-0818
presumptive pronephric mesoderm4.35e-0818
cavitated compound organ5.53e-0832
lung6.14e-0822
respiratory tube6.14e-0822
respiration organ6.14e-0822
pair of lungs6.14e-0822
lung primordium6.14e-0822
lung bud6.14e-0822
viscus8.85e-0818
excretory tube1.54e-0717
mesonephric epithelium1.54e-0717
mesonephric tubule1.54e-0717
nephric duct1.54e-0717
kidney epithelium1.54e-0717
renal duct1.54e-0717
mesonephric duct1.54e-0717
pronephric duct1.54e-0717
intraembryonic coelom2.75e-0721
abdomen element2.78e-0755
abdominal segment element2.78e-0755
mucosa3.20e-0712
multi-tissue structure3.31e-07347
nephron epithelium6.60e-0716
nephron6.60e-0716
uriniferous tubule6.60e-0716
metanephric mesenchyme6.60e-0716
nephrogenic mesenchyme6.60e-0716
urogenital ridge6.74e-0720
mesenchyme7.26e-07238
entire embryonic mesenchyme7.26e-07238
biliary system8.20e-077
biliary tree8.20e-077
biliary bud8.20e-077
Disease
Ontology termp-valuen
carcinoma2.89e-19106
adenocarcinoma1.84e-1225
cell type cancer2.12e-11143
respiratory system cancer2.33e-0716
squamous cell carcinoma6.74e-0714
cancer6.84e-07235


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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