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Coexpression cluster:C1211: Difference between revisions

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|ontology_enrichment_disease=DOID:305!8.85e-16!106;DOID:120!1.45e-14!27;DOID:193!5.17e-13!29;DOID:0050687!2.25e-11!143;DOID:2394!3.95e-11!14;DOID:14566!3.82e-09!239;DOID:299!2.74e-08!25;DOID:162!1.26e-07!235
|ontology_enrichment_disease=DOID:305!8.85e-16!106;DOID:120!1.45e-14!27;DOID:193!5.17e-13!29;DOID:0050687!2.25e-11!143;DOID:2394!3.95e-11!14;DOID:14566!3.82e-09!239;DOID:299!2.74e-08!25;DOID:162!1.26e-07!235
|ontology_enrichment_uberon=UBERON:0004119!7.42e-14!169;UBERON:0000925!7.42e-14!169;UBERON:0006595!7.42e-14!169;UBERON:0004921!3.55e-13!129;UBERON:0004185!3.55e-13!129;UBERON:0005156!7.54e-13!59;UBERON:0000990!7.54e-13!59;UBERON:0003134!7.64e-13!37;UBERON:0000474!7.64e-13!37;UBERON:0006554!1.96e-12!44;UBERON:0001008!6.08e-12!45;UBERON:0001007!9.20e-12!155;UBERON:0001555!9.20e-12!155;UBERON:0007026!9.20e-12!155;UBERON:0003100!9.84e-11!41;UBERON:0000466!2.73e-10!126;UBERON:0003133!1.66e-09!48;UBERON:0000077!2.26e-09!130;UBERON:0002553!3.51e-09!70;UBERON:0003886!3.75e-09!63;UBERON:0005172!5.91e-09!55;UBERON:0005173!5.91e-09!55;UBERON:0005409!8.07e-09!35;UBERON:0000992!8.18e-09!13;UBERON:0000160!2.92e-08!27;UBERON:0009773!4.96e-08!12;UBERON:0001231!4.96e-08!12;UBERON:0004810!4.96e-08!12;UBERON:0000464!5.56e-08!104;UBERON:0002113!5.86e-08!27;UBERON:0003918!5.86e-08!27;UBERON:0005095!5.86e-08!27;UBERON:0007687!5.86e-08!27;UBERON:0004211!9.51e-08!16;UBERON:0001285!9.51e-08!16;UBERON:0007684!9.51e-08!16;UBERON:0003220!9.51e-08!16;UBERON:0004208!9.51e-08!16;UBERON:0002417!3.29e-07!61;UBERON:0000916!3.29e-07!61;UBERON:0003064!4.16e-07!37;UBERON:0006555!4.45e-07!17;UBERON:0005103!4.45e-07!17;UBERON:0000083!4.45e-07!17;UBERON:0009201!4.45e-07!17;UBERON:0004819!4.45e-07!17;UBERON:0006553!4.45e-07!17;UBERON:0003074!4.45e-07!17;UBERON:0003060!4.45e-07!17;UBERON:0000058!5.52e-07!26;UBERON:0005177!7.18e-07!107
|ontology_enrichment_uberon=UBERON:0004119!7.42e-14!169;UBERON:0000925!7.42e-14!169;UBERON:0006595!7.42e-14!169;UBERON:0004921!3.55e-13!129;UBERON:0004185!3.55e-13!129;UBERON:0005156!7.54e-13!59;UBERON:0000990!7.54e-13!59;UBERON:0003134!7.64e-13!37;UBERON:0000474!7.64e-13!37;UBERON:0006554!1.96e-12!44;UBERON:0001008!6.08e-12!45;UBERON:0001007!9.20e-12!155;UBERON:0001555!9.20e-12!155;UBERON:0007026!9.20e-12!155;UBERON:0003100!9.84e-11!41;UBERON:0000466!2.73e-10!126;UBERON:0003133!1.66e-09!48;UBERON:0000077!2.26e-09!130;UBERON:0002553!3.51e-09!70;UBERON:0003886!3.75e-09!63;UBERON:0005172!5.91e-09!55;UBERON:0005173!5.91e-09!55;UBERON:0005409!8.07e-09!35;UBERON:0000992!8.18e-09!13;UBERON:0000160!2.92e-08!27;UBERON:0009773!4.96e-08!12;UBERON:0001231!4.96e-08!12;UBERON:0004810!4.96e-08!12;UBERON:0000464!5.56e-08!104;UBERON:0002113!5.86e-08!27;UBERON:0003918!5.86e-08!27;UBERON:0005095!5.86e-08!27;UBERON:0007687!5.86e-08!27;UBERON:0004211!9.51e-08!16;UBERON:0001285!9.51e-08!16;UBERON:0007684!9.51e-08!16;UBERON:0003220!9.51e-08!16;UBERON:0004208!9.51e-08!16;UBERON:0002417!3.29e-07!61;UBERON:0000916!3.29e-07!61;UBERON:0003064!4.16e-07!37;UBERON:0006555!4.45e-07!17;UBERON:0005103!4.45e-07!17;UBERON:0000083!4.45e-07!17;UBERON:0009201!4.45e-07!17;UBERON:0004819!4.45e-07!17;UBERON:0006553!4.45e-07!17;UBERON:0003074!4.45e-07!17;UBERON:0003060!4.45e-07!17;UBERON:0000058!5.52e-07!26;UBERON:0005177!7.18e-07!107
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}}
}}

Revision as of 12:49, 5 September 2012


Full id: C1211_small_lung_bile_clear_colon_rectal_tubular



Phase1 CAGE Peaks

Hg19::chr15:59903975..59903992,+p1@GCNT3
Hg19::chr15:59903999..59904006,+p13@GCNT3
Hg19::chr15:59904021..59904030,+p8@GCNT3
Hg19::chr15:59904033..59904043,+p14@GCNT3
Hg19::chr15:59904045..59904065,+p3@GCNT3
Hg19::chr15:59904077..59904099,+p2@GCNT3
Hg19::chr15:59904110..59904119,+p11@GCNT3


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 cell3.06e-13254
kidney cell1.20e-0918
kidney epithelial cell1.20e-0918
kidney tubule cell4.96e-0812
nephron tubule epithelial cell4.96e-0812
epithelial cell of nephron9.51e-0816
stromal cell2.98e-0727
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure7.42e-14169
endoderm7.42e-14169
presumptive endoderm7.42e-14169
subdivision of digestive tract3.55e-13129
endodermal part of digestive tract3.55e-13129
reproductive structure7.54e-1359
reproductive system7.54e-1359
female reproductive organ7.64e-1337
female reproductive system7.64e-1337
urinary system structure1.96e-1244
renal system6.08e-1245
digestive system9.20e-12155
digestive tract9.20e-12155
primitive gut9.20e-12155
female organism9.84e-1141
immaterial anatomical entity2.73e-10126
reproductive organ1.66e-0948
mixed endoderm/mesoderm-derived structure2.26e-09130
anatomical cavity3.51e-0970
body cavity precursor3.75e-0963
abdomen element5.91e-0955
abdominal segment element5.91e-0955
gastrointestinal system8.07e-0935
female gonad8.18e-0913
intestine2.92e-0827
renal tubule4.96e-0812
nephron tubule4.96e-0812
nephron tubule epithelium4.96e-0812
anatomical space5.56e-08104
kidney5.86e-0827
kidney mesenchyme5.86e-0827
kidney rudiment5.86e-0827
kidney field5.86e-0827
nephron epithelium9.51e-0816
nephron9.51e-0816
uriniferous tubule9.51e-0816
metanephric mesenchyme9.51e-0816
nephrogenic mesenchyme9.51e-0816
abdominal segment of trunk3.29e-0761
abdomen3.29e-0761
intermediate mesoderm4.16e-0737
excretory tube4.45e-0717
mesonephric epithelium4.45e-0717
mesonephric tubule4.45e-0717
nephric duct4.45e-0717
kidney epithelium4.45e-0717
renal duct4.45e-0717
mesonephric duct4.45e-0717
pronephric duct4.45e-0717
duct5.52e-0726
trunk region element7.18e-07107
Disease
Ontology termp-valuen
carcinoma8.85e-16106
female reproductive organ cancer1.45e-1427
reproductive organ cancer5.17e-1329
cell type cancer2.25e-11143
ovarian cancer3.95e-1114
disease of cellular proliferation3.82e-09239
adenocarcinoma2.74e-0825
cancer1.26e-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
EP300#203376.77394172622321.52695018318475e-065.86298346256001e-05
FOSL2#2355716.93020060456172.50368126508949e-092.11726289590835e-07
FOXA1#3169711.08141974938554.86782131208363e-083.14403457027027e-06
FOXA2#3170724.63046375266521.81353313360781e-101.89025535869128e-08
HEY1#2346274.040111043105715.68979821988558e-050.00095032278312271
MAFF#23764756.31535648994525.53198247536579e-138.02437107978789e-11
MAFK#7975727.10073313782999.28633553538878e-111.01237536219256e-08
NR3C1#2908714.9730233311735.91757635984462e-094.70339237021166e-07
POLR2A#543072.147453176558070.004747636447610280.0223411013315297
STAT1#6772720.70658749719926.11318612876182e-105.85201692118933e-08
STAT3#6774710.51946499715427.00768600129688e-084.25014935127436e-06
USF1#739176.361499277207962.37038582734158e-068.4032832797599e-05
USF2#7392712.99219738506961.59819543071901e-081.16804711398784e-06



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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