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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3208_epithelioid_anaplastic_Pancreatic_mucinous_mesenchymal_endometrial_occipital
|full_id=C3208_epithelioid_anaplastic_Pancreatic_mucinous_mesenchymal_endometrial_occipital
|id=C3208
|id=C3208

Revision as of 16:05, 12 September 2012


Full id: C3208_epithelioid_anaplastic_Pancreatic_mucinous_mesenchymal_endometrial_occipital



Phase1 CAGE Peaks

Hg19::chr11:85429930..85429939,-p14@SYTL2
Hg19::chr11:85429940..85429951,-p10@SYTL2
Hg19::chr11:85429982..85430028,-p4@SYTL2


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>

Uber Anatomy
Ontology termp-valuen
central nervous system2.39e-2382
neural tube1.82e-2257
neural rod1.82e-2257
future spinal cord1.82e-2257
neural keel1.82e-2257
organism subdivision2.29e-22365
regional part of nervous system2.71e-2194
nervous system2.71e-2194
brain4.51e-2069
future brain4.51e-2069
regional part of brain2.93e-1959
neural plate1.18e-1886
presumptive neural plate1.18e-1886
adult organism1.95e-17115
neurectoderm8.65e-1790
gray matter1.05e-1634
brain grey matter1.05e-1634
telencephalon3.32e-1634
cerebral hemisphere6.47e-1632
regional part of telencephalon1.69e-1533
head2.09e-15123
anterior region of body2.23e-15129
craniocervical region2.23e-15129
regional part of forebrain6.28e-1541
forebrain6.28e-1541
future forebrain6.28e-1541
ectoderm-derived structure1.72e-14169
anterior neural tube2.98e-1442
somite3.45e-1483
paraxial mesoderm3.45e-1483
presomitic mesoderm3.45e-1483
presumptive segmental plate3.45e-1483
trunk paraxial mesoderm3.45e-1483
presumptive paraxial mesoderm3.45e-1483
ectoderm1.85e-13173
presumptive ectoderm1.85e-13173
cerebral cortex3.35e-1325
pallium3.35e-1325
epithelium3.99e-13309
cell layer1.37e-12312
multi-tissue structure1.54e-12347
regional part of cerebral cortex6.50e-1222
dermomyotome8.27e-1270
pre-chordal neural plate2.62e-1161
neocortex8.70e-1120
muscle tissue3.40e-1063
musculature3.40e-1063
musculature of body3.40e-1063
posterior neural tube7.11e-1015
chordal neural plate7.11e-1015
multilaminar epithelium7.72e-1082
skeletal muscle tissue9.16e-1061
striated muscle tissue9.16e-1061
myotome9.16e-1061
anatomical system2.51e-09625
anatomical group3.34e-09626
skin of body8.89e-0940
multi-cellular organism1.42e-08659
integument1.85e-0845
integumental system1.85e-0845
segmental subdivision of hindbrain3.32e-0812
hindbrain3.32e-0812
presumptive hindbrain3.32e-0812
tube5.88e-08194
segmental subdivision of nervous system3.09e-0713


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
EP300#203336.77394172622320.003216880500103790.0166981999279493
JUN#3725312.51282919233630.0005103313992726250.00443193921575201
JUND#372736.994663941871030.002921845042734990.0156249142047209
STAT3#6774310.51946499715420.0008589184530415310.00641571909005896



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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