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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4057_prostate_smallcell_Mammary_mucinous_pituitary_Keratinocyte_bile
|full_id=C4057_prostate_smallcell_Mammary_mucinous_pituitary_Keratinocyte_bile
|id=C4057
|id=C4057

Revision as of 17:05, 12 September 2012


Full id: C4057_prostate_smallcell_Mammary_mucinous_pituitary_Keratinocyte_bile



Phase1 CAGE Peaks

Hg19::chr20:58411012..58411026,+p7@PHACTR3
Hg19::chr20:58411027..58411085,+p3@PHACTR3
Hg19::chr20:58411232..58411249,+p15@PHACTR3


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
endo-epithelial cell2.83e-1043
respiratory epithelial cell1.27e-0813
endodermal cell6.74e-0759
Uber Anatomy
Ontology termp-valuen
adult organism1.39e-41115
neural tube2.23e-3557
neural rod2.23e-3557
future spinal cord2.23e-3557
neural keel2.23e-3557
regional part of forebrain4.40e-2941
forebrain4.40e-2941
future forebrain4.40e-2941
regional part of brain3.28e-2859
anterior neural tube4.85e-2842
central nervous system1.08e-2582
neural plate6.09e-2586
presumptive neural plate6.09e-2586
regional part of nervous system7.27e-2594
nervous system7.27e-2594
brain1.21e-2369
future brain1.21e-2369
neurectoderm6.63e-2390
ectoderm-derived structure7.40e-23169
gray matter8.67e-2334
brain grey matter8.67e-2334
telencephalon1.07e-2234
regional part of telencephalon5.68e-2233
ectoderm1.17e-21173
presumptive ectoderm1.17e-21173
cerebral hemisphere9.07e-2132
pre-chordal neural plate2.73e-2061
anterior region of body6.19e-20129
craniocervical region6.19e-20129
head1.23e-18123
regional part of cerebral cortex4.18e-1822
neocortex4.67e-1620
cerebral cortex4.77e-1525
pallium4.77e-1525
organ part3.62e-11219
anatomical group6.86e-10626
organ7.66e-10511
anatomical system1.25e-09625
basal ganglion1.46e-099
nuclear complex of neuraxis1.46e-099
aggregate regional part of brain1.46e-099
collection of basal ganglia1.46e-099
cerebral subcortex1.46e-099
nucleus of brain1.65e-099
neural nucleus1.65e-099
cell layer2.22e-09312
multi-cellular organism2.37e-09659
epithelium4.43e-09309
organism subdivision9.30e-09365
posterior neural tube1.80e-0815
chordal neural plate1.80e-0815
anatomical conduit2.64e-08241
embryo2.82e-08612
embryonic structure3.73e-08605
developing anatomical structure3.73e-08605
diencephalon5.78e-087
future diencephalon5.78e-087
germ layer7.95e-08604
embryonic tissue7.95e-08604
presumptive structure7.95e-08604
epiblast (generic)7.95e-08604
telencephalic nucleus1.05e-077
multi-tissue structure1.36e-07347
anatomical cluster4.22e-07286
brainstem7.34e-078
segmental subdivision of nervous system9.73e-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
ZNF263#1012738.221841637010680.001799043925565870.0109595396956471



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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