Coexpression cluster:C3186

Full id: C3186_putamen_cerebellum_acute_caudate_brain_amygdala_temporal

Phase1 CAGE Peaks

Hg19::chr11:64411156..64411192,-	p5@NRXN2
Hg19::chr11:64411195..64411222,-	p6@NRXN2
Hg19::chr2:100938957..100938968,-	p4@LONRF2

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:0006510	ATP-dependent proteolysis	0.0153822753973291
GO:0005246	calcium channel regulator activity	0.0153822753973291
GO:0004176	ATP-dependent peptidase activity	0.0153822753973291
GO:0007416	synaptogenesis	0.0188282299490645
GO:0016247	channel regulator activity	0.0188282299490645
GO:0050808	synapse organization and biogenesis	0.0188282299490645
GO:0007269	neurotransmitter secretion	0.0188282299490645
GO:0045055	regulated secretory pathway	0.0218247999485838
GO:0003001	generation of a signal involved in cell-cell signaling	0.0251450577024572
GO:0001505	regulation of neurotransmitter levels	0.0251450577024572
GO:0043062	extracellular structure organization and biogenesis	0.0251450577024572

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	2.56e-57	56
neural rod	2.56e-57	56
future spinal cord	2.56e-57	56
neural keel	2.56e-57	56
central nervous system	4.25e-54	81
regional part of nervous system	1.77e-53	53
regional part of brain	1.77e-53	53
nervous system	4.04e-52	89
adult organism	3.45e-49	114
brain	1.03e-45	68
future brain	1.03e-45	68
regional part of forebrain	4.15e-45	41
forebrain	4.15e-45	41
anterior neural tube	4.15e-45	41
future forebrain	4.15e-45	41
telencephalon	1.49e-41	34
brain grey matter	1.76e-41	34
gray matter	1.76e-41	34
neural plate	2.26e-40	82
presumptive neural plate	2.26e-40	82
cerebral hemisphere	2.21e-39	32
neurectoderm	4.26e-39	86
regional part of telencephalon	6.02e-39	32
regional part of cerebral cortex	4.04e-34	22
neocortex	3.66e-31	20
ecto-epithelium	9.43e-31	104
pre-chordal neural plate	1.69e-29	61
cerebral cortex	3.44e-29	25
pallium	3.44e-29	25
ectoderm-derived structure	8.39e-26	171
ectoderm	8.39e-26	171
presumptive ectoderm	8.39e-26	171
structure with developmental contribution from neural crest	2.49e-25	132
organ system subdivision	4.31e-24	223
basal ganglion	3.41e-14	9
nuclear complex of neuraxis	3.41e-14	9
aggregate regional part of brain	3.41e-14	9
collection of basal ganglia	3.41e-14	9
cerebral subcortex	3.41e-14	9
neural nucleus	1.11e-13	9
nucleus of brain	1.11e-13	9
posterior neural tube	5.02e-13	15
chordal neural plate	5.02e-13	15
anatomical cluster	5.25e-13	373
temporal lobe	1.47e-11	6
telencephalic nucleus	2.96e-11	7
tube	4.62e-11	192
gyrus	4.62e-10	6
segmental subdivision of hindbrain	1.34e-09	12
hindbrain	1.34e-09	12
presumptive hindbrain	1.34e-09	12
anatomical conduit	2.20e-09	240
limbic system	5.41e-09	5
brainstem	5.53e-09	6
organ part	7.00e-09	218
segmental subdivision of nervous system	1.10e-08	13
parietal lobe	1.16e-08	5
occipital lobe	1.33e-08	5
corpus striatum	9.15e-08	4
striatum	9.15e-08	4
ventral part of telencephalon	9.15e-08	4
future corpus striatum	9.15e-08	4
multi-tissue structure	1.14e-07	342

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293299960402298

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.