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{{Coexpression_clusters
 
{{Coexpression_clusters
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|full_id=C3316_Amniotic_seminal_ductal_ductus_lung_tubular_Placental
 
|full_id=C3316_Amniotic_seminal_ductal_ductus_lung_tubular_Placental
 
|id=C3316
 
|id=C3316

Revision as of 07:13, 12 September 2012


Full id: C3316_Amniotic_seminal_ductal_ductus_lung_tubular_Placental



Phase1 CAGE Peaks

  Short description
Hg19::chr12:6484190..6484221,- p7@SCNN1A
Hg19::chr12:6484243..6484261,- p10@SCNN1A
Hg19::chr12:6484306..6484392,+ p4@LTBR


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
epithelial cell3.00e-19254
endo-epithelial cell1.69e-1243
endodermal cell3.72e-1259
respiratory epithelial cell1.92e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.90e-24169
endoderm4.90e-24169
presumptive endoderm4.90e-24169
subdivision of digestive tract2.20e-20129
endodermal part of digestive tract2.20e-20129
digestive system1.49e-18155
digestive tract1.49e-18155
primitive gut1.49e-18155
mixed endoderm/mesoderm-derived structure1.87e-17130
immaterial anatomical entity3.43e-16126
anatomical space6.36e-16104
trunk region element2.38e-15107
foregut1.26e-1398
multi-tissue structure1.48e-12347
mesenchyme3.91e-11238
entire embryonic mesenchyme3.91e-11238
respiratory system1.68e-1072
primordium9.22e-10168
endo-epithelium9.80e-1082
respiratory tract1.17e-0953
thoracic cavity element1.32e-0934
thoracic cavity1.32e-0934
organ segment1.47e-0997
renal system1.82e-0945
urinary system structure3.56e-0944
embryo3.61e-09612
thoracic segment organ4.83e-0935
respiratory primordium7.22e-0938
endoderm of foregut7.22e-0938
subdivision of trunk9.31e-09113
organ1.29e-08511
epithelial bud2.74e-0837
intestine2.77e-0827
multi-cellular organism5.30e-08659
anatomical cavity5.65e-0870
gastrointestinal system7.42e-0835
duct1.16e-0726
embryonic structure1.57e-07605
developing anatomical structure1.57e-07605
lung2.03e-0722
respiratory tube2.03e-0722
respiration organ2.03e-0722
pair of lungs2.03e-0722
lung primordium2.03e-0722
lung bud2.03e-0722
organ part2.20e-07219
germ layer2.83e-07604
embryonic tissue2.83e-07604
presumptive structure2.83e-07604
epiblast (generic)2.83e-07604
segment of respiratory tract7.27e-0746
Disease
Ontology termp-valuen
carcinoma2.48e-12106
cell type cancer1.00e-08143
adenocarcinoma7.65e-0725


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ESR1#2099220.51240219743630.003099741577095180.0163040849400807



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.