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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2585_somatostatinoma_parotid_small_pancreas_smallcell_Alveolar_salivary
|full_id=C2585_somatostatinoma_parotid_small_pancreas_smallcell_Alveolar_salivary
|id=C2585
|id=C2585

Revision as of 15:20, 12 September 2012


Full id: C2585_somatostatinoma_parotid_small_pancreas_smallcell_Alveolar_salivary



Phase1 CAGE Peaks

Hg19::chr1:43736324..43736409,+p1@TMEM125
Hg19::chr1:43751230..43751274,-p1@C1orf210
Hg19::chr1:43751276..43751293,-p2@C1orf210
Hg19::chr6:27218970..27219009,+p2@PRSS16


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
epithelial cell3.22e-29254
endo-epithelial cell2.68e-1443
endodermal cell6.39e-1459
epithelial cell of alimentary canal1.43e-0721
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.11e-25169
endoderm1.11e-25169
presumptive endoderm1.11e-25169
digestive system3.63e-21155
digestive tract3.63e-21155
primitive gut3.63e-21155
subdivision of digestive tract4.91e-21129
endodermal part of digestive tract4.91e-21129
mixed endoderm/mesoderm-derived structure1.55e-18130
respiratory system3.21e-1472
foregut1.06e-1398
anatomical space1.80e-12104
immaterial anatomical entity3.76e-12126
respiratory tract1.86e-1153
trunk region element2.76e-11107
endo-epithelium7.59e-1182
respiratory primordium8.84e-1038
endoderm of foregut8.84e-1038
epithelial bud4.18e-0937
renal system7.67e-0945
urinary system structure1.59e-0844
gastrointestinal system1.60e-0835
segment of respiratory tract2.06e-0846
organ part1.23e-07219
subdivision of trunk1.59e-07113
epithelial fold3.50e-0751
thoracic segment organ3.97e-0735
thoracic cavity element5.30e-0734
thoracic cavity5.30e-0734
anatomical cavity7.14e-0770
lung7.76e-0722
respiratory tube7.76e-0722
respiration organ7.76e-0722
pair of lungs7.76e-0722
lung primordium7.76e-0722
lung bud7.76e-0722
orifice9.03e-0735
Disease
Ontology termp-valuen
carcinoma3.43e-29106
cell type cancer1.17e-20143
cancer1.53e-10235
adenocarcinoma3.21e-1025
disease of cellular proliferation1.57e-09239
squamous cell carcinoma3.08e-0814


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
BCL3#602217.27355140186920.004834494208076070.0226762660826937
FOXA2#3170212.31523187633260.009361916285467240.0353475714883017
HNF4A#3172211.56614518147680.01057585681762490.0390735782572495
HNF4G#3174214.37671126322340.006924169980439180.0293071282102163
TAF1#687243.343046285745290.008005664898701650.0322496195462278



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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