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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4841_Mesothelial_gastrointestinal_Hepatocyte_oral_small_signet_liver
|full_id=C4841_Mesothelial_gastrointestinal_Hepatocyte_oral_small_signet_liver
|id=C4841
|id=C4841

Revision as of 17:59, 12 September 2012


Full id: C4841_Mesothelial_gastrointestinal_Hepatocyte_oral_small_signet_liver



Phase1 CAGE Peaks

Hg19::chrX:105969873..105969884,+p5@RNF128
Hg19::chrX:105969893..105969919,+p2@RNF128
Hg19::chrX:105969923..105969947,+p1@RNF128


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><br>

Cell Type
Ontology termp-valuen
endodermal cell4.83e-1259
endo-epithelial cell1.23e-0843
Uber Anatomy
Ontology termp-valuen
organism subdivision2.14e-19365
multi-tissue structure1.61e-18347
adult organism3.39e-15115
ectoderm-derived structure2.99e-13169
ectoderm3.15e-13173
presumptive ectoderm3.15e-13173
endoderm-derived structure6.67e-13169
endoderm6.67e-13169
presumptive endoderm6.67e-13169
neural tube7.57e-1357
neural rod7.57e-1357
future spinal cord7.57e-1357
neural keel7.57e-1357
central nervous system1.70e-1282
anterior region of body4.35e-12129
craniocervical region4.35e-12129
epithelium5.15e-12309
regional part of nervous system5.23e-1294
nervous system5.23e-1294
anterior neural tube6.07e-1242
head7.28e-12123
multi-cellular organism7.77e-12659
regional part of forebrain8.02e-1241
forebrain8.02e-1241
future forebrain8.02e-1241
embryo1.48e-11612
cell layer2.44e-11312
embryonic structure4.35e-11605
developing anatomical structure4.35e-11605
anatomical conduit4.42e-11241
germ layer4.73e-11604
embryonic tissue4.73e-11604
presumptive structure4.73e-11604
epiblast (generic)4.73e-11604
digestive system5.97e-11155
digestive tract5.97e-11155
primitive gut5.97e-11155
anatomical group7.66e-11626
anatomical system8.37e-11625
regional part of brain9.18e-1159
organ9.61e-11511
brain1.80e-1069
future brain1.80e-1069
gray matter1.95e-1034
brain grey matter1.95e-1034
telencephalon1.99e-1034
cerebral hemisphere2.31e-1032
subdivision of digestive tract4.88e-10129
endodermal part of digestive tract4.88e-10129
regional part of telencephalon5.44e-1033
neural plate1.44e-0986
presumptive neural plate1.44e-0986
neurectoderm1.89e-0990
tube1.99e-09194
pre-chordal neural plate2.38e-0961
endo-epithelium8.19e-0982
cerebral cortex4.12e-0825
pallium4.12e-0825
gland4.56e-0859
gut epithelium8.88e-0854
anatomical cluster1.03e-07286
regional part of cerebral cortex1.11e-0722
exocrine gland2.35e-0731
exocrine system2.35e-0731
neocortex3.24e-0720
mixed endoderm/mesoderm-derived structure7.09e-07130


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
REST#597839.650028716128020.001112636247114590.00772213031714518



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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