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|full_id=C4609_Esophageal_Urothelial_Mesothelial_bile_epidermoid_Mesenchymal_gastric
|full_id=C4609_Esophageal_Urothelial_Mesothelial_bile_epidermoid_Mesenchymal_gastric
|id=C4609
|id=C4609
|ontology_enrichment_celltype=CL:0000066!1.63e-16!254;CL:0000223!4.22e-10!59;CL:0002076!4.91e-10!43;CL:0000220!9.16e-10!246;CL:0002321!1.18e-09!248
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000467!4.45e-30!625;UBERON:0000480!1.47e-29!626;UBERON:0000468!5.01e-29!659;UBERON:0000922!1.30e-24!612;UBERON:0002050!2.60e-24!605;UBERON:0005423!2.60e-24!605;UBERON:0000923!5.26e-24!604;UBERON:0005291!5.26e-24!604;UBERON:0006598!5.26e-24!604;UBERON:0002532!5.26e-24!604;UBERON:0004111!1.64e-23!241;UBERON:0000062!3.12e-20!511;UBERON:0000475!5.42e-19!365;UBERON:0000025!7.00e-19!194;UBERON:0000119!1.80e-18!312;UBERON:0000477!2.06e-18!286;UBERON:0000483!7.54e-18!309;UBERON:0000481!1.49e-14!347;UBERON:0002100!7.24e-13!216;UBERON:0004119!3.75e-12!169;UBERON:0000925!3.75e-12!169;UBERON:0006595!3.75e-12!169;UBERON:0003914!9.33e-12!118;UBERON:0000064!1.10e-11!219;UBERON:0000466!1.30e-11!126;UBERON:0001007!2.30e-09!155;UBERON:0001555!2.30e-09!155;UBERON:0007026!2.30e-09!155;UBERON:0003104!2.43e-09!238;UBERON:0009142!2.43e-09!238;UBERON:0000926!3.49e-09!448;UBERON:0004120!3.49e-09!448;UBERON:0006603!3.49e-09!448;UBERON:0000464!4.40e-09!104;UBERON:0004921!1.16e-08!129;UBERON:0004185!1.16e-08!129;UBERON:0009569!2.55e-08!113;UBERON:0005177!4.74e-08!107;UBERON:0005256!7.84e-08!143;UBERON:0000077!9.65e-08!130;UBERON:0004121!4.99e-07!169;UBERON:0005911!5.82e-07!82;UBERON:0001017!7.99e-07!82;UBERON:0000490!9.14e-07!138
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Revision as of 14:50, 21 May 2012


Full id: C4609_Esophageal_Urothelial_Mesothelial_bile_epidermoid_Mesenchymal_gastric



Phase1 CAGE Peaks

Hg19::chr6:47277594..47277605,-p4@TNFRSF21
Hg19::chr6:47277620..47277631,-p3@TNFRSF21
Hg19::chr6:47277634..47277651,-p1@TNFRSF21


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><br>

Cell Type
Ontology termp-valuen
epithelial cell1.63e-16254
endodermal cell4.22e-1059
endo-epithelial cell4.91e-1043
embryonic cell1.18e-09248
Uber Anatomy
Ontology termp-valuen
anatomical system4.45e-30625
anatomical group1.47e-29626
multi-cellular organism5.01e-29659
embryo1.30e-24612
embryonic structure2.60e-24605
developing anatomical structure2.60e-24605
germ layer5.26e-24604
embryonic tissue5.26e-24604
presumptive structure5.26e-24604
epiblast (generic)5.26e-24604
anatomical conduit1.64e-23241
organ3.12e-20511
organism subdivision5.42e-19365
tube7.00e-19194
cell layer1.80e-18312
anatomical cluster2.06e-18286
epithelium7.54e-18309
multi-tissue structure1.49e-14347
trunk7.24e-13216
endoderm-derived structure3.75e-12169
endoderm3.75e-12169
presumptive endoderm3.75e-12169
epithelial tube9.33e-12118
organ part1.10e-11219
immaterial anatomical entity1.30e-11126
digestive system2.30e-09155
digestive tract2.30e-09155
primitive gut2.30e-09155
mesenchyme2.43e-09238
entire embryonic mesenchyme2.43e-09238
mesoderm3.49e-09448
mesoderm-derived structure3.49e-09448
presumptive mesoderm3.49e-09448
anatomical space4.40e-09104
subdivision of digestive tract1.16e-08129
endodermal part of digestive tract1.16e-08129
subdivision of trunk2.55e-08113
trunk region element4.74e-08107
trunk mesenchyme7.84e-08143
mixed endoderm/mesoderm-derived structure9.65e-08130
ectoderm-derived structure4.99e-07169
endo-epithelium5.82e-0782
central nervous system7.99e-0782
unilaminar epithelium9.14e-07138


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

No analysis results for this cluster

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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