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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1489_colon_Hepatocyte_liver_small_adenocarcinoma_hepatocellular_duodenum
|full_id=C1489_colon_Hepatocyte_liver_small_adenocarcinoma_hepatocellular_duodenum
|id=C1489
|id=C1489

Revision as of 14:03, 12 September 2012


Full id: C1489_colon_Hepatocyte_liver_small_adenocarcinoma_hepatocellular_duodenum



Phase1 CAGE Peaks

Hg19::chr21:44859375..44859383,-p@chr21:44859375..44859383
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Hg19::chr2:88425813..88425828,-p2@BX641099
Hg19::chr2:88425833..88425845,-p1@BX641099
Hg19::chr2:88427571..88427590,-p1@FABP1
Hg19::chr3:195943369..195943392,+p2@OSTalpha
Hg19::chr5:66307148..66307152,-p@chr5:66307148..66307152
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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
metabolising cell9.33e-0912
endopolyploid cell9.33e-0912
parenchymal cell9.33e-0912
polyploid cell9.33e-0912
hepatocyte9.33e-0912
embryonic stem cell4.48e-085
Uber Anatomy
Ontology termp-valuen
subdivision of digestive tract8.84e-23129
endodermal part of digestive tract8.84e-23129
endoderm-derived structure7.26e-21169
endoderm7.26e-21169
presumptive endoderm7.26e-21169
digestive system1.11e-20155
digestive tract1.11e-20155
primitive gut1.11e-20155
mixed endoderm/mesoderm-derived structure1.63e-17130
foregut3.75e-1498
epithelium of foregut-midgut junction3.26e-1325
anatomical boundary3.26e-1325
hepatobiliary system3.26e-1325
foregut-midgut junction3.26e-1325
septum transversum3.26e-1325
gut epithelium1.25e-1254
immune organ1.29e-1226
digestive tract diverticulum1.29e-1123
adult organism2.00e-11115
sac2.32e-1126
liver5.50e-1119
digestive gland5.50e-1119
liver bud5.50e-1119
hepatic diverticulum2.02e-1022
liver primordium2.02e-1022
endo-epithelium2.35e-1082
epithelial sac3.20e-1025
immaterial anatomical entity2.36e-09126
abdomen element2.98e-0955
abdominal segment element2.98e-0955
respiratory tract9.80e-0953
trunk region element1.04e-08107
larynx1.27e-089
multi-tissue structure2.01e-08347
mesenchyme2.69e-08238
entire embryonic mesenchyme2.69e-08238
endocrine gland2.80e-0835
gastrointestinal system4.09e-0835
respiratory system7.59e-0872
abdominal segment of trunk9.93e-0861
abdomen9.93e-0861
primordium1.04e-07168
upper respiratory tract1.09e-0719
exocrine gland1.39e-0731
exocrine system1.39e-0731
intestine1.64e-0727
large intestine2.37e-0711
gland3.14e-0759
multi-cellular organism3.95e-07659
embryo4.12e-07612


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
HEY1#2346253.366759202588090.004423827045203030.0209532912822657



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.