Coexpression cluster:C4167

Full id: C4167_parietal_temporal_occipital_duodenum_putamen_pituitary_neuroectodermal

Phase1 CAGE Peaks

Hg19::chr2:197791441..197791525,-	p1@PGAP1
Hg19::chrX:73439688..73439692,-	p@chrX:73439688..73439692 -
Hg19::chrX:73513353..73513414,-	p1@FTX

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:0015798	myo-inositol transport	0.00294360061226893
GO:0015791	polyol transport	0.00367950076533615
GO:0006505	GPI anchor metabolic process	0.0152086031633895
GO:0031227	intrinsic to endoplasmic reticulum membrane	0.0224449546685506
GO:0030384	phosphoinositide metabolic process	0.0235488048981514
GO:0006650	glycerophospholipid metabolic process	0.0247753051532635
GO:0031300	intrinsic to organelle membrane	0.0319590923617769
GO:0006644	phospholipid metabolic process	0.0395546332273637
GO:0004518	nuclease activity	0.0400329683268574
GO:0006643	membrane lipid metabolic process	0.0400329683268574

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>

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Uber Anatomy

Ontology term	p-value	n
adult organism	6.94e-35	114
nervous system	4.33e-30	89
central nervous system	9.38e-30	81
neural tube	1.18e-28	56
neural rod	1.18e-28	56
future spinal cord	1.18e-28	56
neural keel	1.18e-28	56
regional part of nervous system	6.63e-27	53
regional part of brain	6.63e-27	53
brain	1.25e-25	68
future brain	1.25e-25	68
regional part of forebrain	4.48e-24	41
forebrain	4.48e-24	41
anterior neural tube	4.48e-24	41
future forebrain	4.48e-24	41
brain grey matter	4.02e-20	34
gray matter	4.02e-20	34
telencephalon	4.49e-20	34
neurectoderm	3.63e-19	86
cerebral hemisphere	3.99e-19	32
regional part of telencephalon	4.33e-19	32
neural plate	4.68e-18	82
presumptive neural plate	4.68e-18	82
ectoderm-derived structure	7.28e-17	171
ectoderm	7.28e-17	171
presumptive ectoderm	7.28e-17	171
cerebral cortex	5.57e-15	25
pallium	5.57e-15	25
regional part of cerebral cortex	1.09e-14	22
organ system subdivision	2.54e-14	223
pre-chordal neural plate	1.34e-13	61
neocortex	1.97e-13	20
ecto-epithelium	1.29e-11	104
structure with developmental contribution from neural crest	1.30e-09	132
basal ganglion	6.57e-07	9
nuclear complex of neuraxis	6.57e-07	9
aggregate regional part of brain	6.57e-07	9
collection of basal ganglia	6.57e-07	9
cerebral subcortex	6.57e-07	9

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.