Coexpression cluster:C787

Full id: C787_cerebellum_pons_locus_brain_medulla_paracentral_temporal

Phase1 CAGE Peaks

Hg19::chr10:73848474..73848491,-	p10@SPOCK2
Hg19::chr11:105480740..105480750,+	p9@GRIA4
Hg19::chr15:79724672..79724683,+	p1@KIAA1024
Hg19::chr17:26902537..26902548,-	p3@ALDOC
Hg19::chr17:26903863..26903893,-	p2@ALDOC
Hg19::chr1:111148241..111148250,-	p25@KCNA2
Hg19::chr1:111148637..111148657,-	p7@KCNA2
Hg19::chr22:47016277..47016290,+	p4@GRAMD4
Hg19::chr3:9745510..9745528,+	p1@CPNE9
Hg19::chr5:175308178..175308191,+	p18@CPLX2

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:0043303	mast cell degranulation	0.0362732334316763
GO:0002448	mast cell mediated immunity	0.0362732334316763
GO:0045576	mast cell activation	0.0362732334316763
GO:0043299	leukocyte degranulation	0.0362732334316763
GO:0004332	fructose-bisphosphate aldolase activity	0.0362732334316763
GO:0002444	myeloid leukocyte mediated immunity	0.0362732334316763
GO:0005251	delayed rectifier potassium channel activity	0.0376409746877379
GO:0016832	aldehyde-lyase activity	0.0376409746877379
GO:0022836	gated channel activity	0.0376409746877379
GO:0019905	syntaxin binding	0.0376409746877379
GO:0000149	SNARE binding	0.0376409746877379
GO:0007215	glutamate signaling pathway	0.0376409746877379
GO:0006000	fructose metabolic process	0.0376409746877379
GO:0007416	synaptogenesis	0.0376409746877379
GO:0002274	myeloid leukocyte activation	0.0376409746877379
GO:0005216	ion channel activity	0.0376409746877379
GO:0022838	substrate specific channel activity	0.0376409746877379
GO:0022803	passive transmembrane transporter activity	0.0376409746877379
GO:0015267	channel activity	0.0376409746877379
GO:0006904	vesicle docking during exocytosis	0.0376409746877379
GO:0004970	ionotropic glutamate receptor activity	0.0376409746877379
GO:0048278	vesicle docking	0.0376409746877379
GO:0022406	membrane docking	0.0376409746877379
GO:0050808	synapse organization and biogenesis	0.0376409746877379
GO:0005234	extracellular-glutamate-gated ion channel activity	0.0376409746877379
GO:0030198	extracellular matrix organization and biogenesis	0.0426674863585992
GO:0045055	regulated secretory pathway	0.0473152348550167

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
neural tube	1.94e-28	57
neural rod	1.94e-28	57
future spinal cord	1.94e-28	57
neural keel	1.94e-28	57
regional part of nervous system	1.57e-24	94
nervous system	1.57e-24	94
central nervous system	2.10e-24	82
regional part of brain	2.83e-23	59
regional part of forebrain	1.62e-22	41
forebrain	1.62e-22	41
future forebrain	1.62e-22	41
anterior neural tube	3.73e-22	42
adult organism	1.42e-21	115
neural plate	4.21e-21	86
presumptive neural plate	4.21e-21	86
brain	6.86e-21	69
future brain	6.86e-21	69
neurectoderm	3.45e-20	90
gray matter	1.48e-18	34
brain grey matter	1.48e-18	34
telencephalon	1.61e-18	34
regional part of telencephalon	7.39e-18	33
cerebral hemisphere	2.27e-17	32
pre-chordal neural plate	2.95e-16	61
regional part of cerebral cortex	2.82e-15	22
neocortex	4.25e-14	20
cerebral cortex	3.45e-13	25
pallium	3.45e-13	25
tube	4.39e-11	194
anterior region of body	2.30e-10	129
craniocervical region	2.30e-10	129
head	1.04e-09	123
ectoderm-derived structure	1.37e-09	169
ectoderm	2.25e-09	173
presumptive ectoderm	2.25e-09	173
posterior neural tube	1.84e-07	15
chordal neural plate	1.84e-07	15
anatomical cluster	2.04e-07	286
anatomical conduit	2.27e-07	241
nucleus of brain	6.56e-07	9
neural nucleus	6.56e-07	9
basal ganglion	7.99e-07	9
nuclear complex of neuraxis	7.99e-07	9
aggregate regional part of brain	7.99e-07	9
collection of basal ganglia	7.99e-07	9
cerebral subcortex	7.99e-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)
{{{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.