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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3845_ductus_seminal_smallcell_colon_epididymis_salivary_pancreas
|full_id=C3845_ductus_seminal_smallcell_colon_epididymis_salivary_pancreas
|id=C3845
|id=C3845

Revision as of 16:49, 12 September 2012


Full id: C3845_ductus_seminal_smallcell_colon_epididymis_salivary_pancreas



Phase1 CAGE Peaks

Hg19::chr1:1098252..1098265,+p@chr1:1098252..1098265
+
Hg19::chr1:1098315..1098328,+p@chr1:1098315..1098328
+
Hg19::chr3:121741065..121741106,-p1@ILDR1


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>

Cell Type
Ontology termp-valuen
endo-epithelial cell3.70e-1643
epithelial cell3.02e-14254
endodermal cell1.27e-1159
respiratory epithelial cell4.57e-0913
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.96e-22169
endoderm3.96e-22169
presumptive endoderm3.96e-22169
digestive system2.16e-18155
digestive tract2.16e-18155
primitive gut2.16e-18155
subdivision of digestive tract9.23e-16129
endodermal part of digestive tract9.23e-16129
anatomical space2.70e-15104
immaterial anatomical entity1.65e-13126
mixed endoderm/mesoderm-derived structure9.36e-13130
endo-epithelium2.52e-1182
respiratory system3.18e-1172
renal system1.75e-1045
trunk region element2.56e-10107
urinary system structure6.66e-1044
thoracic cavity element3.18e-0934
thoracic cavity3.18e-0934
thoracic segment organ9.01e-0935
respiratory tract2.53e-0853
reproductive structure2.74e-0859
reproductive system2.74e-0859
duct3.30e-0826
orifice3.87e-0835
subdivision of trunk4.10e-08113
intermediate mesoderm4.19e-0837
epithelial bud5.05e-0837
foregut6.89e-0898
anatomical cavity1.03e-0770
gastrointestinal system1.11e-0735
lung2.29e-0722
respiratory tube2.29e-0722
respiration organ2.29e-0722
pair of lungs2.29e-0722
lung primordium2.29e-0722
lung bud2.29e-0722
male organism5.42e-0722
male reproductive system5.42e-0722
mucosa5.43e-0712
reproductive organ7.78e-0748
thoracic segment of trunk7.95e-0752
internal genitalia8.88e-0725
Disease
Ontology termp-valuen
carcinoma1.31e-14106
squamous cell carcinoma2.13e-1014
cell type cancer1.23e-08143
adenocarcinoma1.97e-0825


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
ESR1#2099220.51240219743630.003099741577095180.0163098347811095



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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