Coexpression cluster:C738

Full id: C738_locus_spinal_globus_thalamus_medulla_hippocampus_medial

Phase1 CAGE Peaks

Hg19::chr11:43963775..43963782,-	p@chr11:43963775..43963782 -
Hg19::chr11:65324915..65324925,+	p@chr11:65324915..65324925 +
Hg19::chr13:20938911..20938912,+	p@chr13:20938911..20938912 +
Hg19::chr14:55068991..55068998,+	p@chr14:55068991..55068998 +
Hg19::chr15:34260755..34260766,+	p3@CHRM5
Hg19::chr15:65359631..65359643,+	p@chr15:65359631..65359643 +
Hg19::chr18:72240382..72240391,+	p9@CNDP1
Hg19::chr22:35918540..35918560,+	p@chr22:35918540..35918560 +
Hg19::chr8:82352747..82352757,-	p@chr8:82352747..82352757 -
Hg19::chr8:8794478..8794485,+	p@chr8:8794478..8794485 +
Hg19::chr9:71961268..71961288,+	p@chr9:71961268..71961288 +

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:0007197	muscarinic acetylcholine receptor, adenylate cyclase inhibiting pathway	0.00906535579451634
GO:0015872	dopamine transport	0.00906535579451634
GO:0007213	acetylcholine receptor signaling, muscarinic pathway	0.00906535579451634
GO:0004981	muscarinic acetylcholine receptor activity	0.00906535579451634
GO:0007193	G-protein signaling, adenylate cyclase inhibiting pathway	0.0142426233902423
GO:0015464	acetylcholine receptor activity	0.0142426233902423
GO:0042166	acetylcholine binding	0.0142426233902423
GO:0043176	amine binding	0.0203859415236058
GO:0004435	phosphoinositide phospholipase C activity	0.0203859415236058
GO:0004434	inositol or phosphatidylinositol phosphodiesterase activity	0.0203859415236058
GO:0004629	phospholipase C activity	0.0234705717213597
GO:0008227	amine receptor activity	0.0246177753104829
GO:0004180	carboxypeptidase activity	0.0246177753104829
GO:0006836	neurotransmitter transport	0.0246177753104829
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0246177753104829
GO:0019933	cAMP-mediated signaling	0.0246177753104829
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.0280819695540108
GO:0004620	phospholipase activity	0.0280819695540108
GO:0019935	cyclic-nucleotide-mediated signaling	0.0280819695540108
GO:0008081	phosphoric diester hydrolase activity	0.0280819695540108
GO:0030594	neurotransmitter receptor activity	0.0280819695540108
GO:0016298	lipase activity	0.0280819695540108
GO:0042165	neurotransmitter binding	0.0280819695540108
GO:0045211	postsynaptic membrane	0.0280819695540108
GO:0044456	synapse part	0.029124704314621
GO:0008238	exopeptidase activity	0.0313102748621034
GO:0004091	carboxylesterase activity	0.0313102748621034
GO:0016787	hydrolase activity	0.0368690161900824
GO:0019932	second-messenger-mediated signaling	0.0417278817504469
GO:0019226	transmission of nerve impulse	0.0496231317780302

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
brainstem	2.38e-74	6
pons	3.13e-54	3
posterior neural tube	6.16e-43	15
chordal neural plate	6.16e-43	15
neural tube	1.74e-37	56
neural rod	1.74e-37	56
future spinal cord	1.74e-37	56
neural keel	1.74e-37	56
segmental subdivision of hindbrain	2.25e-37	12
hindbrain	2.25e-37	12
presumptive hindbrain	2.25e-37	12
locus ceruleus	4.73e-37	2
brainstem nucleus	4.73e-37	2
hindbrain nucleus	4.73e-37	2
segmental subdivision of nervous system	1.59e-34	13
regional part of nervous system	1.31e-32	53
regional part of brain	1.31e-32	53
neural nucleus	2.42e-32	9
nucleus of brain	2.42e-32	9
central nervous system	1.34e-25	81
neural plate	1.34e-25	82
presumptive neural plate	1.34e-25	82
brain	4.73e-25	68
future brain	4.73e-25	68
medulla oblongata	7.02e-25	3
myelencephalon	7.02e-25	3
future myelencephalon	7.02e-25	3
neurectoderm	2.13e-24	86
nervous system	4.81e-23	89
ecto-epithelium	4.01e-20	104
putamen	3.25e-19	1
regional part of metencephalon	1.25e-18	9
metencephalon	1.25e-18	9
future metencephalon	1.25e-18	9
adult organism	1.73e-18	114
brain grey matter	2.01e-18	34
gray matter	2.01e-18	34
structure with developmental contribution from neural crest	9.24e-16	132
ectoderm-derived structure	6.88e-12	171
ectoderm	6.88e-12	171
presumptive ectoderm	6.88e-12	171
telencephalic nucleus	2.83e-11	7
regional part of forebrain	7.69e-11	41
forebrain	7.69e-11	41
anterior neural tube	7.69e-11	41
future forebrain	7.69e-11	41
tube	1.20e-10	192
dorsal plus ventral thalamus	1.89e-10	2
thalamic complex	1.89e-10	2
globus pallidus	2.07e-10	2
pallidum	2.07e-10	2
Ammon's horn	2.27e-10	2
lobe parts of cerebral cortex	2.27e-10	2
hippocampal formation	2.27e-10	2
limbic lobe	2.27e-10	2
middle temporal gyrus	2.49e-10	2
regional part of telencephalon	4.42e-09	32
cerebral hemisphere	4.42e-09	32
basal ganglion	5.64e-09	9
nuclear complex of neuraxis	5.64e-09	9
aggregate regional part of brain	5.64e-09	9
collection of basal ganglia	5.64e-09	9
cerebral subcortex	5.64e-09	9
organ system subdivision	6.17e-09	223
telencephalon	1.41e-08	34
anatomical conduit	2.27e-08	240
spinal cord	1.93e-07	3
dorsal region element	1.93e-07	3
dorsum	1.93e-07	3
pre-chordal neural plate	2.36e-07	61
caudate-putamen	2.79e-07	3
dorsal striatum	2.79e-07	3

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)
{{{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

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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.