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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4322_occipital_frontal_insula_medial_olfactory_aorta_serous
|full_id=C4322_occipital_frontal_insula_medial_olfactory_aorta_serous
|id=C4322
|id=C4322

Revision as of 17:23, 12 September 2012


Full id: C4322_occipital_frontal_insula_medial_olfactory_aorta_serous



Phase1 CAGE Peaks

Hg19::chr3:24536253..24536328,-p1@THRB
Hg19::chr3:24536332..24536358,-p2@THRB
Hg19::chr3:24536516..24536545,-p6@THRB


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.78e-39115
neural tube3.55e-2257
neural rod3.55e-2257
future spinal cord3.55e-2257
neural keel3.55e-2257
organ1.17e-21511
anterior neural tube1.29e-2042
regional part of forebrain5.62e-2041
forebrain5.62e-2041
future forebrain5.62e-2041
regional part of brain3.12e-1859
central nervous system3.68e-1882
brain1.61e-1769
future brain1.61e-1769
telencephalon2.56e-1734
gray matter2.85e-1734
brain grey matter2.85e-1734
organism subdivision3.19e-17365
cerebral hemisphere6.95e-1732
regional part of telencephalon1.19e-1633
regional part of cerebral cortex1.24e-1622
multi-tissue structure9.87e-16347
organ part1.01e-15219
neocortex1.76e-1520
ectoderm-derived structure9.42e-15169
neural plate1.50e-1486
presumptive neural plate1.50e-1486
regional part of nervous system2.21e-1494
nervous system2.21e-1494
endoderm-derived structure2.02e-13169
endoderm2.02e-13169
presumptive endoderm2.02e-13169
ectoderm3.19e-13173
presumptive ectoderm3.19e-13173
head3.27e-13123
cerebral cortex4.64e-1325
pallium4.64e-1325
multi-cellular organism5.40e-13659
anterior region of body5.47e-13129
craniocervical region5.47e-13129
digestive system6.45e-13155
digestive tract6.45e-13155
primitive gut6.45e-13155
pre-chordal neural plate2.10e-1261
neurectoderm2.22e-1290
anatomical system1.44e-11625
anatomical group2.48e-11626
subdivision of digestive tract7.80e-11129
endodermal part of digestive tract7.80e-11129
mixed endoderm/mesoderm-derived structure4.20e-09130
embryo5.23e-08612
anatomical cluster2.04e-07286
embryonic structure2.47e-07605
developing anatomical structure2.47e-07605
germ layer3.22e-07604
embryonic tissue3.22e-07604
presumptive structure3.22e-07604
epiblast (generic)3.22e-07604
temporal lobe7.88e-077
epithelium9.51e-07309


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
CCNT2#90536.336201576962630.003930750035764890.0190639733902317
CTCF#1066435.360256373075030.0064925092527670.0280519267685642
E2F6#187635.017155731697390.00791769806886330.0323456471196563
TFAP2C#7022310.80922860986020.0007916746575753130.00617580740682015
ZNF263#1012738.221841637010680.001799043925565870.0109736215712051



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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