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Coexpression cluster:C3909: Difference between revisions

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|full_id=C3909_Hepatocyte_gastrointestinal_signet_liver_argyrophil_pancreas_gastric
|full_id=C3909_Hepatocyte_gastrointestinal_signet_liver_argyrophil_pancreas_gastric
|id=C3909
|id=C3909
|ontology_enrichment_celltype=CL:1000507!4.23e-11!12;CL:1000494!4.23e-11!12;CL:0000181!6.05e-11!12;CL:0000417!6.05e-11!12;CL:0000668!6.05e-11!12;CL:0000414!6.05e-11!12;CL:0000412!6.05e-11!12;CL:0000182!6.05e-11!12;CL:1000497!2.27e-10!18;CL:0002518!2.27e-10!18;CL:1000449!7.16e-08!16;CL:0000223!6.44e-07!59
|ontology_enrichment_celltype=CL:0000181!1.19e-16!12;CL:0000417!1.19e-16!12;CL:0000668!1.19e-16!12;CL:0000412!1.19e-16!12;CL:0000182!1.19e-16!12;CL:0000223!2.50e-10!58;CL:1000507!6.52e-10!10;CL:1000494!6.52e-10!10;CL:1000497!2.07e-07!17;CL:0002518!2.07e-07!17;CL:0000650!8.65e-07!2;CL:1000500!8.65e-07!2;CL:1000618!8.65e-07!2;CL:1001318!8.65e-07!2;CL:0002173!8.65e-07!2
|ontology_enrichment_disease=DOID:299!1.85e-10!25;DOID:305!1.52e-08!106
|ontology_enrichment_disease=DOID:299!1.42e-12!25;DOID:305!1.35e-09!106;DOID:3493!1.51e-07!2;DOID:4468!8.15e-07!2
|ontology_enrichment_uberon=UBERON:0005172!3.87e-21!55;UBERON:0005173!3.87e-21!55;UBERON:0002417!1.04e-19!61;UBERON:0000916!1.04e-19!61;UBERON:0004921!2.41e-18!129;UBERON:0004185!2.41e-18!129;UBERON:0005409!4.63e-17!35;UBERON:0005177!9.14e-17!107;UBERON:0000466!3.69e-16!126;UBERON:0009854!4.56e-15!23;UBERON:0001007!4.11e-14!155;UBERON:0001555!4.11e-14!155;UBERON:0007026!4.11e-14!155;UBERON:0008835!1.21e-13!22;UBERON:0003894!1.21e-13!22;UBERON:0009497!1.58e-13!25;UBERON:0000015!1.58e-13!25;UBERON:0002423!1.58e-13!25;UBERON:0006235!1.58e-13!25;UBERON:0004161!1.58e-13!25;UBERON:0009569!3.01e-13!113;UBERON:0009856!7.14e-13!26;UBERON:0000160!9.26e-13!27;UBERON:0004119!1.19e-12!169;UBERON:0000925!1.19e-12!169;UBERON:0006595!1.19e-12!169;UBERON:0005057!2.03e-12!26;UBERON:0000077!6.81e-12!130;UBERON:0002107!7.42e-12!19;UBERON:0006925!7.42e-12!19;UBERON:0008836!7.42e-12!19;UBERON:0007499!1.40e-11!25;UBERON:0009773!4.23e-11!12;UBERON:0001231!4.23e-11!12;UBERON:0004810!4.23e-11!12;UBERON:0002113!7.42e-11!27;UBERON:0003918!7.42e-11!27;UBERON:0005095!7.42e-11!27;UBERON:0007687!7.42e-11!27;UBERON:0003887!3.91e-10!21;UBERON:0000489!6.28e-10!32;UBERON:0000058!2.51e-09!26;UBERON:0001008!2.56e-09!45;UBERON:0003104!2.94e-09!238;UBERON:0009142!2.94e-09!238;UBERON:0006555!3.10e-09!17;UBERON:0005103!3.10e-09!17;UBERON:0000083!3.10e-09!17;UBERON:0009201!3.10e-09!17;UBERON:0004819!3.10e-09!17;UBERON:0006553!3.10e-09!17;UBERON:0003074!3.10e-09!17;UBERON:0003060!3.10e-09!17;UBERON:0003929!5.38e-09!54;UBERON:0000949!8.13e-09!45;UBERON:0001041!8.22e-09!98;UBERON:0000080!1.33e-08!18;UBERON:0002120!1.33e-08!18;UBERON:0004875!1.33e-08!18;UBERON:0005721!1.33e-08!18;UBERON:0005754!1.33e-08!18;UBERON:0007297!1.33e-08!18;UBERON:0000059!1.76e-08!11;UBERON:0006554!1.92e-08!44;UBERON:0002368!2.28e-08!35;UBERON:0003886!2.38e-08!63;UBERON:0000481!2.98e-08!347;UBERON:0002553!6.62e-08!70;UBERON:0004211!7.16e-08!16;UBERON:0001285!7.16e-08!16;UBERON:0007684!7.16e-08!16;UBERON:0003220!7.16e-08!16;UBERON:0004208!7.16e-08!16;UBERON:0000464!9.41e-08!104;UBERON:0005911!9.56e-08!82;UBERON:0002100!1.34e-07!216;UBERON:0004876!1.57e-07!20;UBERON:0002365!2.85e-07!31;UBERON:0002330!2.85e-07!31;UBERON:0004175!3.07e-07!25;UBERON:0003064!9.27e-07!37;UBERON:0004907!9.38e-07!5
|ontology_enrichment_uberon=UBERON:0005172!1.76e-22!54;UBERON:0005173!1.76e-22!54;UBERON:0002417!1.20e-19!60;UBERON:0000916!1.20e-19!60;UBERON:0009854!4.15e-18!23;UBERON:0005409!9.41e-18!25;UBERON:0005177!1.06e-16!101;UBERON:0009497!2.17e-16!25;UBERON:0000015!2.17e-16!25;UBERON:0002423!2.17e-16!25;UBERON:0006235!2.17e-16!25;UBERON:0004161!2.17e-16!25;UBERON:0004921!3.66e-16!118;UBERON:0008835!4.92e-16!22;UBERON:0003894!4.92e-16!22;UBERON:0000160!5.32e-16!17;UBERON:0002107!1.04e-15!19;UBERON:0006925!1.04e-15!19;UBERON:0008836!1.04e-15!19;UBERON:0009856!1.10e-15!26;UBERON:0007499!8.36e-14!25;UBERON:0001007!8.40e-13!145;UBERON:0001555!8.40e-13!145;UBERON:0007026!8.40e-13!145;UBERON:0009569!6.07e-12!112;UBERON:0003929!1.66e-11!54;UBERON:0000466!3.45e-11!117;UBERON:0004119!6.75e-11!160;UBERON:0000925!6.75e-11!160;UBERON:0006595!6.75e-11!160;UBERON:0000059!6.15e-10!11;UBERON:0004810!6.52e-10!10;UBERON:0002113!1.16e-09!26;UBERON:0003918!1.16e-09!26;UBERON:0011143!1.16e-09!26;UBERON:0005095!1.16e-09!26;UBERON:0007687!1.16e-09!26;UBERON:0000949!2.68e-09!45;UBERON:0005911!2.86e-09!82;UBERON:0002368!4.15e-09!35;UBERON:0002365!8.66e-09!31;UBERON:0002330!8.66e-09!31;UBERON:0001155!1.08e-08!9;UBERON:0006555!4.02e-08!16;UBERON:0004819!4.02e-08!16;UBERON:0000489!8.57e-08!31;UBERON:0003104!1.82e-07!160;UBERON:0009142!1.82e-07!160;UBERON:0001041!2.40e-07!87;UBERON:0002100!3.91e-07!199;UBERON:0000481!5.88e-07!342;UBERON:0011216!7.48e-07!223;UBERON:0003567!8.65e-07!2;UBERON:0003838!8.65e-07!2;UBERON:0003586!8.65e-07!2;UBERON:0005169!8.65e-07!2;UBERON:0002321!8.65e-07!2;UBERON:0005215!8.65e-07!2;UBERON:0002303!8.65e-07!2;UBERON:0002319!8.65e-07!2
|tf_chipseq_enrich=BCL11A#53335;2:18.9129700690714:0.00363940624837968:0.0183887735449698!ESR1#2099;2:20.5124021974363:0.00309974157709518:0.0163114783377963!FOXA2#3170;2:16.4203091684435:0.00481068235210548:0.0225899399384715!NANOG#79923;2:19.4965189873418:0.00342725564850102:0.0174493810107638!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460454459836475!RXRA#6256;2:13.3830780927555:0.00719643442946573:0.0298320399848762!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276974050455138!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246682311553878
|tf_chipseq_enrich=BCL11A#53335;2:18.9129700690714:0.00363940624837968:0.0183887735449698!ESR1#2099;2:20.5124021974363:0.00309974157709518:0.0163114783377963!FOXA2#3170;2:16.4203091684435:0.00481068235210548:0.0225899399384715!NANOG#79923;2:19.4965189873418:0.00342725564850102:0.0174493810107638!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460454459836475!RXRA#6256;2:13.3830780927555:0.00719643442946573:0.0298320399848762!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276974050455138!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246682311553878
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}}
}}

Revision as of 15:30, 19 October 2012


Full id: C3909_Hepatocyte_gastrointestinal_signet_liver_argyrophil_pancreas_gastric



Phase1 CAGE Peaks

Hg19::chr1:17906970..17906994,+p5@ARHGEF10L
Hg19::chr7:47510248..47510266,-p@chr7:47510248..47510266
-
Hg19::chr7:47510275..47510293,-p@chr7:47510275..47510293
-


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
abdomen element1.76e-2254
abdominal segment element1.76e-2254
abdominal segment of trunk1.20e-1960
abdomen1.20e-1960
digestive tract diverticulum4.15e-1823
gastrointestinal system9.41e-1825
trunk region element1.06e-16101
epithelium of foregut-midgut junction2.17e-1625
anatomical boundary2.17e-1625
hepatobiliary system2.17e-1625
foregut-midgut junction2.17e-1625
septum transversum2.17e-1625
subdivision of digestive tract3.66e-16118
hepatic diverticulum4.92e-1622
liver primordium4.92e-1622
intestine5.32e-1617
liver1.04e-1519
digestive gland1.04e-1519
liver bud1.04e-1519
sac1.10e-1526
epithelial sac8.36e-1425
digestive system8.40e-13145
digestive tract8.40e-13145
primitive gut8.40e-13145
subdivision of trunk6.07e-12112
gut epithelium1.66e-1154
immaterial anatomical entity3.45e-11117
endoderm-derived structure6.75e-11160
endoderm6.75e-11160
presumptive endoderm6.75e-11160
large intestine6.15e-1011
nephron tubule epithelium6.52e-1010
kidney1.16e-0926
kidney mesenchyme1.16e-0926
upper urinary tract1.16e-0926
kidney rudiment1.16e-0926
kidney field1.16e-0926
endocrine system2.68e-0945
endo-epithelium2.86e-0982
endocrine gland4.15e-0935
exocrine gland8.66e-0931
exocrine system8.66e-0931
colon1.08e-089
excretory tube4.02e-0816
kidney epithelium4.02e-0816
cavitated compound organ8.57e-0831
mesenchyme1.82e-07160
entire embryonic mesenchyme1.82e-07160
foregut2.40e-0787
trunk3.91e-07199
multi-tissue structure5.88e-07342
organ system subdivision7.48e-07223
abdomen connective tissue8.65e-072
abdominal segment connective tissue8.65e-072
trunk connective tissue8.65e-072
interstitial tissue8.65e-072
extraglomerular mesangium8.65e-072
kidney interstitium8.65e-072
juxtaglomerular apparatus8.65e-072
mesangium8.65e-072
Disease
Ontology termp-valuen
adenocarcinoma1.42e-1225
carcinoma1.35e-09106
signet ring cell adenocarcinoma1.51e-072
clear cell adenocarcinoma8.15e-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
BCL11A#53335218.91297006907140.003639406248379680.0183887735449698
ESR1#2099220.51240219743630.003099741577095180.0163114783377963
FOXA2#3170216.42030916844350.004810682352105480.0225899399384715
NANOG#79923219.49651898734180.003427255648501020.0174493810107638
NR3C1#290829.982015554115360.01278474365547170.0460454459836475
RXRA#6256213.38307809275550.007196434429465730.0298320399848762
SIN3A#2594235.408884726815140.006318961977991520.0276974050455138
SP1#666735.69838137814090.005403962701712170.0246682311553878



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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