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Coexpression cluster:C3157

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Full id: C3157_cerebellum_smooth_ductus_occipital_bladder_brain_heart



Phase1 CAGE Peaks

Hg19::chr11:47546146..47546156,-p34@CELF1
Hg19::chr11:47546176..47546188,-p10@CELF1
Hg19::chr22:41763408..41763417,+p5@TEF


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


GO IDGO nameFDR corrected p-value
GO:0003690double-stranded DNA binding0.0487681031437654
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0487681031437654
GO:0043566structure-specific DNA binding0.0487681031437654
GO:0045893positive regulation of transcription, DNA-dependent0.0487681031437654
GO:0003702RNA polymerase II transcription factor activity0.0487681031437654
GO:0045941positive regulation of transcription0.0487681031437654
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0487681031437654
GO:0016563transcription activator activity0.0487681031437654
GO:0031325positive regulation of cellular metabolic process0.0487681031437654
GO:0046983protein dimerization activity0.0487681031437654
GO:0009893positive regulation of metabolic process0.0487681031437654
GO:0006357regulation of transcription from RNA polymerase II promoter0.0487681031437654



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 organism3.06e-54115
neural tube1.74e-2657
neural rod1.74e-2657
future spinal cord1.74e-2657
neural keel1.74e-2657
central nervous system8.24e-2482
regional part of brain1.49e-2359
regional part of nervous system6.27e-2394
nervous system6.27e-2394
brain2.40e-2269
future brain2.40e-2269
neural plate3.65e-2186
presumptive neural plate3.65e-2186
regional part of forebrain1.47e-2041
forebrain1.47e-2041
future forebrain1.47e-2041
neurectoderm3.07e-2090
anterior neural tube8.47e-2042
telencephalon2.28e-1834
neocortex3.15e-1820
regional part of cerebral cortex7.78e-1822
gray matter1.04e-1734
brain grey matter1.04e-1734
regional part of telencephalon2.25e-1733
cerebral hemisphere4.37e-1732
cerebral cortex6.95e-1525
pallium6.95e-1525
pre-chordal neural plate7.17e-1461
anterior region of body7.87e-14129
craniocervical region7.87e-14129
head1.27e-12123
ectoderm-derived structure2.15e-12169
ectoderm4.11e-12173
presumptive ectoderm4.11e-12173
segmental subdivision of nervous system3.08e-0813
organ3.13e-08511
gyrus3.71e-086
posterior neural tube7.52e-0815
chordal neural plate7.52e-0815
temporal lobe1.88e-077
segmental subdivision of hindbrain2.22e-0712
hindbrain2.22e-0712
presumptive hindbrain2.22e-0712


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#1012738.221841637010680.001799043925565870.0108966159335484



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.