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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4031_Small_teratocarcinoma_epididymis_Placental_clear_amniotic_Bronchial
|full_id=C4031_Small_teratocarcinoma_epididymis_Placental_clear_amniotic_Bronchial
|id=C4031
|id=C4031

Revision as of 17:04, 12 September 2012


Full id: C4031_Small_teratocarcinoma_epididymis_Placental_clear_amniotic_Bronchial



Phase1 CAGE Peaks

Hg19::chr20:37230443..37230457,+p3@ARHGAP40
Hg19::chr20:37230495..37230509,+p2@ARHGAP40
Hg19::chr20:37230511..37230530,+p1@ARHGAP40


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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.61e-13169
endoderm1.61e-13169
presumptive endoderm1.61e-13169
anatomical space1.71e-13104
immaterial anatomical entity2.13e-12126
extraembryonic membrane1.14e-1014
membranous layer1.14e-1014
urinary system structure1.11e-0944
renal system2.68e-0945
respiratory system4.31e-0972
mixed endoderm/mesoderm-derived structure2.88e-08130
reproductive structure5.16e-0859
reproductive system5.16e-0859
excretory tube6.60e-0817
mesonephric epithelium6.60e-0817
mesonephric tubule6.60e-0817
nephric duct6.60e-0817
kidney epithelium6.60e-0817
renal duct6.60e-0817
mesonephric duct6.60e-0817
pronephric duct6.60e-0817
digestive system1.11e-07155
digestive tract1.11e-07155
primitive gut1.11e-07155
mucosa1.13e-0712
respiratory tract1.35e-0753
trunk region element1.57e-07107
chorion1.60e-077
anatomical cavity1.69e-0770
male reproductive organ1.88e-0711
urogenital ridge2.18e-0720
thoracic cavity element2.44e-0734
thoracic cavity2.44e-0734
reproductive organ2.58e-0748
mesonephros2.82e-0718
pronephros2.82e-0718
nephrogenic cord2.82e-0718
pronephric mesoderm2.82e-0718
rostral part of nephrogenic cord2.82e-0718
presumptive pronephric mesoderm2.82e-0718
endo-epithelium3.07e-0782
duct4.03e-0726
intermediate mesoderm4.27e-0737
orifice4.40e-0735
thoracic segment organ5.59e-0735
transitional epithelium5.80e-076
nephron epithelium6.42e-0716
nephron6.42e-0716
uriniferous tubule6.42e-0716
metanephric mesenchyme6.42e-0716
nephrogenic mesenchyme6.42e-0716
male organism6.57e-0722
male reproductive system6.57e-0722
renal tubule7.70e-0712
nephron tubule7.70e-0712
nephron tubule epithelium7.70e-0712
Disease
Ontology termp-valuen
squamous cell carcinoma1.87e-0814
carcinoma1.49e-07106


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
CTCF#1066435.360256373075030.0064925092527670.027984778120088
ZBTB7A#5134137.35190930787590.002516255860282270.014040457647701



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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