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Coexpression cluster:C3753

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Full id: C3753_parietal_brain_occipital_Mesenchymal_cerebellum_Neural_temporal



Phase1 CAGE Peaks

Hg19::chr19:13134154..13134180,+p@chr19:13134154..13134180
+
Hg19::chr19:13134191..13134214,+p@chr19:13134191..13134214
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Hg19::chr19:13134457..13134462,+p5@NFIX


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
organism subdivision7.56e-29365
central nervous system1.78e-2582
ectoderm5.30e-25173
presumptive ectoderm5.30e-25173
regional part of nervous system6.88e-2594
nervous system6.88e-2594
neural tube1.03e-2457
neural rod1.03e-2457
future spinal cord1.03e-2457
neural keel1.03e-2457
brain3.23e-2469
future brain3.23e-2469
ectoderm-derived structure4.67e-24169
head9.66e-23123
regional part of brain1.39e-2259
neurectoderm1.96e-2190
anterior region of body6.19e-21129
craniocervical region6.19e-21129
neural plate1.43e-2086
presumptive neural plate1.43e-2086
regional part of forebrain8.46e-1841
forebrain8.46e-1841
future forebrain8.46e-1841
anterior neural tube2.17e-1742
telencephalon5.65e-1734
cell layer1.69e-16312
epithelium1.80e-16309
regional part of telencephalon2.12e-1633
gray matter2.73e-1634
brain grey matter2.73e-1634
cerebral hemisphere9.51e-1632
somite2.96e-1583
paraxial mesoderm2.96e-1583
presomitic mesoderm2.96e-1583
presumptive segmental plate2.96e-1583
trunk paraxial mesoderm2.96e-1583
presumptive paraxial mesoderm2.96e-1583
pre-chordal neural plate3.16e-1461
dermomyotome2.38e-1370
anatomical conduit2.68e-13241
cerebral cortex5.06e-1325
pallium5.06e-1325
tube5.86e-13194
adult organism1.32e-12115
anatomical cluster1.45e-12286
multi-tissue structure2.03e-12347
regional part of cerebral cortex2.28e-1222
skeletal muscle tissue3.99e-1261
striated muscle tissue3.99e-1261
myotome3.99e-1261
muscle tissue8.92e-1263
musculature8.92e-1263
musculature of body8.92e-1263
neocortex1.49e-1120
multilaminar epithelium2.68e-1182
multi-cellular organism1.01e-10659
surface structure5.64e-0995
artery5.75e-0942
arterial blood vessel5.75e-0942
arterial system5.75e-0942
posterior neural tube1.42e-0815
chordal neural plate1.42e-0815
systemic artery1.76e-0833
systemic arterial system1.76e-0833
anatomical system1.94e-08625
anatomical group3.22e-08626
embryonic structure7.15e-08605
developing anatomical structure7.15e-08605
segmental subdivision of nervous system7.57e-0813
germ layer1.05e-07604
embryonic tissue1.05e-07604
presumptive structure1.05e-07604
epiblast (generic)1.05e-07604
integument2.50e-0745
integumental system2.50e-0745
tissue2.89e-07787
segmental subdivision of hindbrain3.46e-0712
hindbrain3.46e-0712
presumptive hindbrain3.46e-0712
embryo4.76e-07612
blood vessel6.44e-0760
epithelial tube open at both ends6.44e-0760
blood vasculature6.44e-0760
vascular cord6.44e-0760


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
CTBP2#1488362.71700033932814.049570681927e-060.000129654540910415
CTCF#1066435.360256373075030.0064925092527670.0279386557004422
E2F6#187635.017155731697390.00791769806886330.0322095769335104
ZNF263#1012738.221841637010680.001799043925565870.0109391213636571
ZZZ3#260092159.6088082901555.21262599582697e-050.000886647306804842



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.