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|ontology_enrichment_disease=DOID:305!2.58e-16!106;DOID:0050687!9.39e-11!143
|ontology_enrichment_disease=DOID:305!2.58e-16!106;DOID:0050687!9.39e-11!143
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|ontology_enrichment_uberon=UBERON:0004119!5.43e-19!169;UBERON:0000925!5.43e-19!169;UBERON:0006595!5.43e-19!169;UBERON:0001007!4.17e-16!155;UBERON:0001555!4.17e-16!155;UBERON:0007026!4.17e-16!155;UBERON:0004921!2.22e-15!129;UBERON:0004185!2.22e-15!129;UBERON:0000481!1.32e-14!347;UBERON:0000064!5.70e-13!219;UBERON:0000077!7.92e-12!130;UBERON:0005911!3.63e-11!82;UBERON:0000062!5.43e-11!511;UBERON:0001041!1.46e-10!98;UBERON:0005177!1.64e-10!107;UBERON:0003104!2.54e-10!238;UBERON:0009142!2.54e-10!238;UBERON:0009569!1.23e-09!113;UBERON:0005172!4.71e-09!55;UBERON:0005173!4.71e-09!55;UBERON:0006554!1.37e-08!44;UBERON:0001004!1.87e-08!72;UBERON:0000466!1.91e-08!126;UBERON:0008947!3.16e-08!38;UBERON:0003258!3.16e-08!38;UBERON:0000922!3.52e-08!612;UBERON:0001008!5.06e-08!45;UBERON:0000065!7.92e-08!53;UBERON:0000468!1.34e-07!659;UBERON:0002417!2.27e-07!61;UBERON:0000916!2.27e-07!61;UBERON:0000475!2.47e-07!365;UBERON:0000467!2.77e-07!625;UBERON:0002050!3.02e-07!605;UBERON:0005423!3.02e-07!605;UBERON:0000923!3.54e-07!604;UBERON:0005291!3.54e-07!604;UBERON:0006598!3.54e-07!604;UBERON:0002532!3.54e-07!604;UBERON:0000480!4.15e-07!626;UBERON:0000483!5.51e-07!309
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}}
}}

Revision as of 20:36, 8 August 2012


Full id: C611_small_hepatocellular_colon_adenocarcinoma_Intestinal_signet_temporal



Phase1 CAGE Peaks

Hg19::chr10:102729876..102729890,-p1@AK000735
Hg19::chr10:102729908..102729938,-p2@AK000735
Hg19::chr13:76335013..76335032,+p14@LMO7
Hg19::chr16:2034715..2034726,+p10@GFER
Hg19::chr16:75284758..75284802,-p@chr16:75284758..75284802
-
Hg19::chr2:233742013..233742020,-p@chr2:233742013..233742020
-
Hg19::chr2:61245275..61245310,-p6@PUS10
Hg19::chr2:74753294..74753302,-p6@DQX1
Hg19::chr2:74753305..74753331,-p2@DQX1
Hg19::chr2:74753332..74753373,-p1@DQX1
Hg19::chr3:8693755..8693789,-p1@C3orf32
Hg19::chr6:158993336..158993351,+p10@TMEM181
Hg19::chr7:55256663..55256679,-p2@ENST00000442411
p2@uc003tqo.2
Hg19::chr9:86571432..86571453,-p5@C9orf64


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


GO IDGO nameFDR corrected p-value
GO:0016972thiol oxidase activity0.0141274113637933
GO:0016670oxidoreductase activity, acting on sulfur group of donors, oxygen as acceptor0.0141274113637933



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 cell1.89e-22254
endodermal cell5.13e-1559
endo-epithelial cell1.85e-1043
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.43e-19169
endoderm5.43e-19169
presumptive endoderm5.43e-19169
digestive system4.17e-16155
digestive tract4.17e-16155
primitive gut4.17e-16155
subdivision of digestive tract2.22e-15129
endodermal part of digestive tract2.22e-15129
multi-tissue structure1.32e-14347
organ part5.70e-13219
mixed endoderm/mesoderm-derived structure7.92e-12130
endo-epithelium3.63e-1182
organ5.43e-11511
foregut1.46e-1098
trunk region element1.64e-10107
mesenchyme2.54e-10238
entire embryonic mesenchyme2.54e-10238
subdivision of trunk1.23e-09113
abdomen element4.71e-0955
abdominal segment element4.71e-0955
urinary system structure1.37e-0844
respiratory system1.87e-0872
immaterial anatomical entity1.91e-08126
respiratory primordium3.16e-0838
endoderm of foregut3.16e-0838
embryo3.52e-08612
renal system5.06e-0845
respiratory tract7.92e-0853
multi-cellular organism1.34e-07659
abdominal segment of trunk2.27e-0761
abdomen2.27e-0761
organism subdivision2.47e-07365
anatomical system2.77e-07625
embryonic structure3.02e-07605
developing anatomical structure3.02e-07605
germ layer3.54e-07604
embryonic tissue3.54e-07604
presumptive structure3.54e-07604
epiblast (generic)3.54e-07604
anatomical group4.15e-07626
epithelium5.51e-07309
Disease
Ontology termp-valuen
carcinoma2.58e-16106
cell type cancer9.39e-11143


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)

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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.