Coexpression cluster:C3078

Full id: C3078_pineal_extraskeletal_occipital_medial_cerebellum_amygdala_parietal

Phase1 CAGE Peaks

Hg19::chr11:105480996..105481007,+	p13@GRIA4
Hg19::chr8:107282368..107282379,+	p5@OXR1
Hg19::chr8:107282389..107282493,+	p1@OXR1

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:0016998	cell wall catabolic process	0.0150194937569828
GO:0010382	cell wall metabolic process	0.0150194937569828
GO:0007047	cell wall organization and biogenesis	0.0150194937569828
GO:0007215	glutamate signaling pathway	0.0150194937569828
GO:0045229	external encapsulating structure organization and biogenesis	0.0150194937569828
GO:0004970	ionotropic glutamate receptor activity	0.019013430069202
GO:0005234	extracellular-glutamate-gated ion channel activity	0.019013430069202
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.0306990760222157
GO:0008066	glutamate receptor activity	0.0356145402287207
GO:0006979	response to oxidative stress	0.0372431402806523
GO:0005230	extracellular ligand-gated ion channel activity	0.0372431402806523
GO:0045211	postsynaptic membrane	0.0372431402806523
GO:0044456	synapse part	0.0372431402806523
GO:0015276	ligand-gated ion channel activity	0.0372431402806523
GO:0022834	ligand-gated channel activity	0.0372431402806523

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	3.87e-11	76
skin fibroblast	2.14e-07	23

Uber Anatomy

Ontology term	p-value	n
central nervous system	2.10e-33	81
nervous system	6.22e-31	89
brain	3.84e-30	68
future brain	3.84e-30	68
neural tube	2.36e-29	56
neural rod	2.36e-29	56
future spinal cord	2.36e-29	56
neural keel	2.36e-29	56
regional part of nervous system	1.17e-27	53
regional part of brain	1.17e-27	53
regional part of forebrain	1.41e-25	41
forebrain	1.41e-25	41
anterior neural tube	1.41e-25	41
future forebrain	1.41e-25	41
neurectoderm	1.82e-21	86
telencephalon	3.28e-21	34
neural plate	7.41e-21	82
presumptive neural plate	7.41e-21	82
ectoderm-derived structure	9.43e-21	171
ectoderm	9.43e-21	171
presumptive ectoderm	9.43e-21	171
brain grey matter	9.86e-21	34
gray matter	9.86e-21	34
cerebral hemisphere	1.37e-20	32
regional part of telencephalon	5.99e-20	32
regional part of cerebral cortex	5.65e-19	22
adult organism	2.23e-18	114
cerebral cortex	5.88e-18	25
pallium	5.88e-18	25
structure with developmental contribution from neural crest	8.15e-18	132
neocortex	2.55e-17	20
pre-chordal neural plate	8.41e-17	61
ecto-epithelium	1.22e-16	104
organ system subdivision	5.18e-16	223
multi-cellular organism	5.50e-09	656
multi-tissue structure	1.04e-08	342
cell layer	5.04e-08	309
anatomical cluster	5.41e-08	373
epithelium	7.60e-08	306
gyrus	5.58e-07	6

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.027822870372563
CTCFL#140690	2	13.1643162393162	0.00743336703699601	0.0306669334377573
MEF2A#4205	2	12.495487273096	0.00823502947802974	0.0324721831781299
MEF2C#4208	2	27.5409029950827	0.00172911993836969	0.010645968121405
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457094773369322
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.0389928757617788

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.