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Coexpression cluster:C1349: Difference between revisions

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|full_id=C1349_Alveolar_bile_chorionic_clear_amniotic_papillotubular_serous
|full_id=C1349_Alveolar_bile_chorionic_clear_amniotic_papillotubular_serous
|id=C1349
|id=C1349
|ontology_enrichment_celltype=CL:0000066!1.90e-27!254;CL:0002076!1.95e-15!43;CL:0000223!1.62e-11!59;CL:0002368!8.22e-11!13;CL:1000507!1.22e-10!12;CL:1000494!1.22e-10!12;CL:1000497!3.43e-09!18;CL:0002518!3.43e-09!18;CL:1000449!3.86e-09!16;CL:0002202!8.92e-07!9;CL:0002632!8.92e-07!9
|ontology_enrichment_celltype=CL:0000066!3.36e-19!253;CL:0002076!1.94e-13!42;CL:0000349!1.38e-12!19;CL:1000507!2.10e-12!10;CL:1000494!2.10e-12!10;CL:1000449!2.02e-10!15;CL:0002541!9.56e-10!3;CL:1000497!5.13e-09!17;CL:0002518!5.13e-09!17;CL:0000239!6.28e-09!3;CL:1000615!6.28e-09!3;CL:0002306!6.28e-09!3;CL:0002368!1.14e-08!13;CL:0000223!1.39e-08!58;CL:0002621!3.65e-08!3;CL:0002681!8.49e-08!12;CL:0002584!8.49e-08!12
|ontology_enrichment_disease=DOID:305!8.49e-11!106
|ontology_enrichment_disease=DOID:305!5.01e-09!106;DOID:4468!7.25e-07!2
|ontology_enrichment_uberon=UBERON:0005911!4.47e-14!82;UBERON:0004119!8.72e-14!169;UBERON:0000925!8.72e-14!169;UBERON:0006595!8.72e-14!169;UBERON:0000058!2.18e-13!26;UBERON:0000464!4.36e-12!104;UBERON:0006554!8.78e-12!44;UBERON:0005631!9.44e-12!14;UBERON:0000158!9.44e-12!14;UBERON:0001008!2.34e-11!45;UBERON:0000065!4.71e-11!53;UBERON:0001004!8.32e-11!72;UBERON:0005178!8.91e-11!34;UBERON:0002224!8.91e-11!34;UBERON:0005153!9.31e-11!37;UBERON:0009773!1.22e-10!12;UBERON:0001231!1.22e-10!12;UBERON:0004810!1.22e-10!12;UBERON:0000466!1.46e-10!126;UBERON:0005181!2.67e-10!35;UBERON:0003064!4.93e-10!37;UBERON:0002048!1.95e-09!22;UBERON:0000117!1.95e-09!22;UBERON:0000171!1.95e-09!22;UBERON:0000170!1.95e-09!22;UBERON:0005597!1.95e-09!22;UBERON:0000118!1.95e-09!22;UBERON:0000064!2.11e-09!219;UBERON:0005177!2.33e-09!107;UBERON:0004876!2.67e-09!20;UBERON:0000080!3.46e-09!18;UBERON:0002120!3.46e-09!18;UBERON:0004875!3.46e-09!18;UBERON:0005721!3.46e-09!18;UBERON:0005754!3.46e-09!18;UBERON:0007297!3.46e-09!18;UBERON:0004211!3.86e-09!16;UBERON:0001285!3.86e-09!16;UBERON:0007684!3.86e-09!16;UBERON:0003220!3.86e-09!16;UBERON:0004208!3.86e-09!16;UBERON:0006555!2.03e-08!17;UBERON:0005103!2.03e-08!17;UBERON:0000083!2.03e-08!17;UBERON:0009201!2.03e-08!17;UBERON:0004819!2.03e-08!17;UBERON:0006553!2.03e-08!17;UBERON:0003074!2.03e-08!17;UBERON:0003060!2.03e-08!17;UBERON:0003124!4.14e-08!7;UBERON:0001007!4.31e-08!155;UBERON:0001555!4.31e-08!155;UBERON:0007026!4.31e-08!155;UBERON:0000077!7.22e-08!130;UBERON:0005157!7.52e-08!51;UBERON:0009569!9.82e-08!113;UBERON:0000365!1.45e-07!5;UBERON:0003887!2.14e-07!21;UBERON:0004807!2.14e-07!28;UBERON:0002294!5.68e-07!7;UBERON:0001173!5.68e-07!7;UBERON:0004912!5.68e-07!7;UBERON:0002113!7.51e-07!27;UBERON:0003918!7.51e-07!27;UBERON:0005095!7.51e-07!27;UBERON:0007687!7.51e-07!27;UBERON:0004923!9.97e-07!57
|ontology_enrichment_uberon=UBERON:0005631!1.10e-21!14;UBERON:0000158!1.10e-21!14;UBERON:0004119!6.14e-17!160;UBERON:0000925!6.14e-17!160;UBERON:0006595!6.14e-17!160;UBERON:0005911!8.99e-16!82;UBERON:0006554!2.74e-15!47;UBERON:0001008!7.25e-15!48;UBERON:0003124!4.88e-14!7;UBERON:0004810!2.10e-12!10;UBERON:0000478!1.52e-11!24;UBERON:0001004!8.09e-11!74;UBERON:0004923!8.74e-11!66;UBERON:0000065!1.03e-10!54;UBERON:0004211!2.02e-10!15;UBERON:0009773!2.02e-10!15;UBERON:0001231!2.02e-10!15;UBERON:0001285!2.02e-10!15;UBERON:0007684!2.02e-10!15;UBERON:0004208!2.02e-10!15;UBERON:0000476!9.56e-10!3;UBERON:0000920!9.56e-10!3;UBERON:0006555!1.13e-09!16;UBERON:0004819!1.13e-09!16;UBERON:0000305!1.53e-09!7;UBERON:0001007!1.72e-09!145;UBERON:0001555!1.72e-09!145;UBERON:0007026!1.72e-09!145;UBERON:0000064!1.93e-09!218;UBERON:0005153!5.41e-09!37;UBERON:0006853!6.28e-09!3;UBERON:0007685!6.28e-09!3;UBERON:0004134!6.28e-09!3;UBERON:0005177!1.56e-08!101;UBERON:0000365!2.00e-08!5;UBERON:0004871!2.70e-08!8;UBERON:0005178!3.32e-08!34;UBERON:0002224!3.32e-08!34;UBERON:0001949!3.65e-08!3;UBERON:0002048!3.90e-08!22;UBERON:0000117!3.90e-08!22;UBERON:0000171!3.90e-08!22;UBERON:0000170!3.90e-08!22;UBERON:0005597!3.90e-08!22;UBERON:0000118!3.90e-08!22;UBERON:0001851!4.82e-08!15;UBERON:0005181!6.74e-08!35;UBERON:0001225!8.49e-08!12;UBERON:0008987!8.49e-08!12;UBERON:0000161!1.71e-07!36;UBERON:0002294!2.63e-07!9;UBERON:0001173!2.63e-07!9;UBERON:0004912!2.63e-07!9;UBERON:0005910!5.13e-07!6;UBERON:0000344!7.24e-07!20
|tf_chipseq_enrich=ESR1#2099;6:30.7686032961545:1.17571957705476e-09:1.07522746854661e-07!FOXA1#3169;6:11.0814197493855:5.39600313513231e-07:2.50468076191148e-05!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0379984091340244!STAT3#6774;5:8.76622083096187:4.28672496720299e-05:0.000766087044575141
|tf_chipseq_enrich=ESR1#2099;6:30.7686032961545:1.17571957705476e-09:1.07522746854661e-07!FOXA1#3169;6:11.0814197493855:5.39600313513231e-07:2.50468076191148e-05!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0379984091340244!STAT3#6774;5:8.76622083096187:4.28672496720299e-05:0.000766087044575141
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}}
}}

Revision as of 11:09, 19 October 2012


Full id: C1349_Alveolar_bile_chorionic_clear_amniotic_papillotubular_serous



Phase1 CAGE Peaks

Hg19::chr11:65778943..65778967,+p2@CST6
Hg19::chr11:65778976..65778988,+p4@CST6
Hg19::chr11:65778994..65779015,+p3@CST6
Hg19::chr11:65779257..65779267,+p6@CST6
Hg19::chr11:65779283..65779289,+p10@CST6
Hg19::chr11:65779378..65779390,+p8@CST6


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
extraembryonic membrane1.10e-2114
membranous layer1.10e-2114
endoderm-derived structure6.14e-17160
endoderm6.14e-17160
presumptive endoderm6.14e-17160
endo-epithelium8.99e-1682
urinary system structure2.74e-1547
renal system7.25e-1548
chorion4.88e-147
nephron tubule epithelium2.10e-1210
extraembryonic structure1.52e-1124
respiratory system8.09e-1174
organ component layer8.74e-1166
respiratory tract1.03e-1054
nephron epithelium2.02e-1015
renal tubule2.02e-1015
nephron tubule2.02e-1015
nephron2.02e-1015
uriniferous tubule2.02e-1015
nephrogenic mesenchyme2.02e-1015
acellular anatomical structure9.56e-103
egg chorion9.56e-103
excretory tube1.13e-0916
kidney epithelium1.13e-0916
amnion1.53e-097
digestive system1.72e-09145
digestive tract1.72e-09145
primitive gut1.72e-09145
organ part1.93e-09218
epithelial bud5.41e-0937
renal cortex tubule6.28e-093
region of nephron tubule6.28e-093
proximal tubule6.28e-093
trunk region element1.56e-08101
urothelium2.00e-085
somatic layer of lateral plate mesoderm2.70e-088
thoracic cavity element3.32e-0834
thoracic cavity3.32e-0834
gingival epithelium3.65e-083
lung3.90e-0822
respiratory tube3.90e-0822
respiration organ3.90e-0822
pair of lungs3.90e-0822
lung primordium3.90e-0822
lung bud3.90e-0822
cortex4.82e-0815
thoracic segment organ6.74e-0835
cortex of kidney8.49e-0812
renal parenchyma8.49e-0812
orifice1.71e-0736
biliary system2.63e-079
biliary tree2.63e-079
biliary bud2.63e-079
transitional epithelium5.13e-076
mucosa7.24e-0720
Disease
Ontology termp-valuen
carcinoma5.01e-09106
clear cell adenocarcinoma7.25e-072


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
ESR1#2099630.76860329615451.17571957705476e-091.07522746854661e-07
FOXA1#3169611.08141974938555.39600313513231e-072.50468076191148e-05
POLR2A#543062.147453176558070.01019570676818780.0379984091340244
STAT3#677458.766220830961874.28672496720299e-050.000766087044575141



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1349&oldid=2247330"