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Coexpression cluster:C2418: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2418_Renal_Urothelial_salivary_Corneal_Bronchial_Mammary_Keratinocyte
|full_id=C2418_Renal_Urothelial_salivary_Corneal_Bronchial_Mammary_Keratinocyte
|id=C2418
|id=C2418

Revision as of 15:08, 12 September 2012


Full id: C2418_Renal_Urothelial_salivary_Corneal_Bronchial_Mammary_Keratinocyte



Phase1 CAGE Peaks

Hg19::chr17:48133330..48133349,+p2@ITGA3
Hg19::chr17:48133352..48133363,+p4@ITGA3
Hg19::chr17:48133424..48133443,+p3@ITGA3
Hg19::chr17:48133459..48133486,+p1@ITGA3


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 cell1.20e-38254
embryonic cell2.14e-32248
mesodermal cell8.14e-16119
squamous epithelial cell6.56e-1362
non-terminally differentiated cell1.66e-12180
endo-epithelial cell1.90e-1243
kidney cell2.72e-1018
kidney epithelial cell2.72e-1018
epithelial cell of nephron1.13e-0916
endodermal cell2.31e-0959
animal cell2.83e-09679
eukaryotic cell2.83e-09679
mesothelial cell5.86e-0919
kidney tubule cell5.53e-0812
nephron tubule epithelial cell5.53e-0812
respiratory epithelial cell5.69e-0813
ecto-epithelial cell6.30e-0833
contractile cell7.60e-0859
kidney cortical cell7.74e-0813
renal cortical epithelial cell7.74e-0813
columnar/cuboidal epithelial cell1.94e-0727
lining cell2.30e-0757
barrier cell2.30e-0757
muscle precursor cell4.24e-0757
myoblast4.24e-0757
multi-potent skeletal muscle stem cell4.24e-0757
ectodermal cell7.86e-0771
Uber Anatomy
Ontology termp-valuen
multi-tissue structure7.49e-20347
organism subdivision1.05e-18365
mesenchyme1.60e-17238
entire embryonic mesenchyme1.60e-17238
cell layer3.30e-16312
epithelium5.58e-16309
trunk1.24e-15216
trunk mesenchyme3.97e-14143
anatomical system2.94e-12625
anatomical group4.18e-12626
multi-cellular organism4.96e-12659
anatomical space1.71e-11104
epithelial tube1.80e-11118
primordium6.93e-11168
immaterial anatomical entity2.42e-10126
anatomical cluster7.86e-10286
nephron epithelium1.13e-0916
nephron1.13e-0916
uriniferous tubule1.13e-0916
metanephric mesenchyme1.13e-0916
nephrogenic mesenchyme1.13e-0916
endoderm-derived structure1.18e-09169
endoderm1.18e-09169
presumptive endoderm1.18e-09169
multilaminar epithelium1.82e-0982
duct2.58e-0926
excretory tube3.28e-0917
mesonephric epithelium3.28e-0917
mesonephric tubule3.28e-0917
nephric duct3.28e-0917
kidney epithelium3.28e-0917
renal duct3.28e-0917
mesonephric duct3.28e-0917
pronephric duct3.28e-0917
vasculature4.16e-0979
vascular system4.16e-0979
unilaminar epithelium4.52e-09138
trunk region element6.33e-09107
parenchyma9.21e-0917
germ layer1.25e-08604
embryonic tissue1.25e-08604
presumptive structure1.25e-08604
epiblast (generic)1.25e-08604
mesonephros1.30e-0818
pronephros1.30e-0818
nephrogenic cord1.30e-0818
pronephric mesoderm1.30e-0818
rostral part of nephrogenic cord1.30e-0818
presumptive pronephric mesoderm1.30e-0818
embryonic structure1.41e-08605
developing anatomical structure1.41e-08605
anatomical conduit2.23e-08241
urogenital ridge2.31e-0820
somite2.75e-0883
paraxial mesoderm2.75e-0883
presomitic mesoderm2.75e-0883
presumptive segmental plate2.75e-0883
trunk paraxial mesoderm2.75e-0883
presumptive paraxial mesoderm2.75e-0883
embryo4.15e-08612
renal tubule5.53e-0812
nephron tubule5.53e-0812
nephron tubule epithelium5.53e-0812
cortex5.86e-0816
ectodermal placode7.17e-0829
anatomical cavity7.64e-0870
cortex of kidney7.74e-0813
renal parenchyma7.74e-0813
organ part8.10e-08219

Disease
Ontology termp-valuen


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#1066445.360256373075030.001211145381643620.00816965785141628
CTCFL#140690419.74647435897446.5732084880439e-060.000192836888000791
EP300#203346.77394172622320.0004748459821442640.0043399351998919
STAT3#6774410.51946499715428.16377768286615e-050.00123086008000701
TAF1#687243.343046285745290.008005664898701650.0321999397810792
TCF7L2#6934410.77017656313737.42969445082454e-050.00115365723870006
YY1#752844.911170749853860.00171871838055440.0106788761346137
ZBTB7A#5134147.35190930787590.000342223540015990.00346365774742998



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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