Coexpression cluster:C4516

Full id: C4516_occipital_duodenum_temporal_Adipocyte_parietal_medial_mixed

Phase1 CAGE Peaks

Hg19::chr5:71504086..71504091,+	p31@MAP1B
Hg19::chr5:71504109..71504117,+	p28@MAP1B
Hg19::chr8:80567172..80567190,+	p5@STMN2

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0030182	neuron differentiation	0.00163934058036349
GO:0048699	generation of neurons	0.00163934058036349
GO:0022008	neurogenesis	0.00163934058036349
GO:0001578	microtubule bundle formation	0.00736372744328584
GO:0007399	nervous system development	0.00736372744328584
GO:0016358	dendrite development	0.00864232922638426
GO:0030426	growth cone	0.00864232922638426
GO:0030427	site of polarized growth	0.00864232922638426
GO:0007026	negative regulation of microtubule depolymerization	0.00864232922638426
GO:0031114	regulation of microtubule depolymerization	0.00864232922638426
GO:0048468	cell development	0.00864232922638426
GO:0007019	microtubule depolymerization	0.00864232922638426
GO:0031111	negative regulation of microtubule polymerization or depolymerization	0.00864232922638426
GO:0031110	regulation of microtubule polymerization or depolymerization	0.010117609612396
GO:0031109	microtubule polymerization or depolymerization	0.0104195146702293
GO:0048731	system development	0.011571990372739
GO:0051261	protein depolymerization	0.0123940198225719
GO:0048869	cellular developmental process	0.0123940198225719
GO:0030154	cell differentiation	0.0123940198225719
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0126950436732381
GO:0048856	anatomical structure development	0.0137607290947746
GO:0007275	multicellular organismal development	0.017270899636267
GO:0051128	regulation of cellular component organization and biogenesis	0.0202965121797894
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0202965121797894
GO:0051248	negative regulation of protein metabolic process	0.0202965121797894
GO:0031175	neurite development	0.0253215333655514
GO:0048666	neuron development	0.0278076846485725
GO:0032502	developmental process	0.0287655222530471
GO:0005875	microtubule associated complex	0.0302493312433866
GO:0032990	cell part morphogenesis	0.0310575802307371
GO:0030030	cell projection organization and biogenesis	0.0310575802307371
GO:0048858	cell projection morphogenesis	0.0310575802307371
GO:0032501	multicellular organismal process	0.0318274926238275
GO:0005625	soluble fraction	0.0335144414387489
GO:0005874	microtubule	0.0414079775642464
GO:0042995	cell projection	0.0414079775642464
GO:0007017	microtubule-based process	0.0414079775642464

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>

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Cell Type

Ontology term	p-value	n
fibroblast	3.03e-13	76
skin fibroblast	2.27e-08	23

Uber Anatomy

Ontology term	p-value	n
nervous system	1.20e-21	89
central nervous system	5.94e-21	81
neural tube	3.42e-20	56
neural rod	3.42e-20	56
future spinal cord	3.42e-20	56
neural keel	3.42e-20	56
regional part of nervous system	1.52e-19	53
regional part of brain	1.52e-19	53
brain grey matter	1.99e-18	34
gray matter	1.99e-18	34
brain	2.67e-18	68
future brain	2.67e-18	68
regional part of forebrain	4.76e-18	41
forebrain	4.76e-18	41
anterior neural tube	4.76e-18	41
future forebrain	4.76e-18	41
telencephalon	8.20e-18	34
regional part of telencephalon	3.30e-17	32
cerebral hemisphere	3.64e-17	32
neural plate	1.63e-15	82
presumptive neural plate	1.63e-15	82
cerebral cortex	2.77e-14	25
pallium	2.77e-14	25
neurectoderm	5.96e-14	86
pre-chordal neural plate	1.11e-13	61
structure with developmental contribution from neural crest	2.45e-12	132
regional part of cerebral cortex	3.95e-12	22
neocortex	5.71e-11	20
ecto-epithelium	6.02e-11	104
ectoderm-derived structure	4.37e-10	171
ectoderm	4.37e-10	171
presumptive ectoderm	4.37e-10	171
tube	1.04e-07	192

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

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
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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

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No analysis results for this cluster

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

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This analysis result is provided for C0 - C305 clusters.