Coexpression cluster:C1860

Full id: C1860_occipital_pineal_medial_parietal_amygdala_caudate_frontal

Phase1 CAGE Peaks

Hg19::chr1:92634472..92634492,+	p1@KIAA1107
Hg19::chr1:92634493..92634508,+	p2@KIAA1107
Hg19::chr2:210444345..210444394,+	p3@MAP2
Hg19::chr5:161580386..161580395,+	p18@GABRG2
Hg19::chrX:38547830..38547849,+	p@chrX:38547830..38547849 +

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:0008503	benzodiazepine receptor activity	0.0230672990440317
GO:0007026	negative regulation of microtubule depolymerization	0.0230672990440317
GO:0031114	regulation of microtubule depolymerization	0.0230672990440317
GO:0007019	microtubule depolymerization	0.0230672990440317
GO:0031111	negative regulation of microtubule polymerization or depolymerization	0.0230672990440317
GO:0007214	gamma-aminobutyric acid signaling pathway	0.0230672990440317
GO:0031110	regulation of microtubule polymerization or depolymerization	0.0230672990440317
GO:0031109	microtubule polymerization or depolymerization	0.0230672990440317
GO:0004890	GABA-A receptor activity	0.0246346270007797
GO:0051261	protein depolymerization	0.0246346270007797
GO:0016917	GABA receptor activity	0.0246346270007797
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0247047731748591
GO:0043168	anion binding	0.0247047731748591
GO:0031404	chloride ion binding	0.0247047731748591
GO:0005254	chloride channel activity	0.0299556956870386
GO:0006821	chloride transport	0.0299556956870386
GO:0051128	regulation of cellular component organization and biogenesis	0.0299556956870386
GO:0005253	anion channel activity	0.0299556956870386
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0299556956870386
GO:0051248	negative regulation of protein metabolic process	0.0299556956870386
GO:0005230	extracellular ligand-gated ion channel activity	0.0337114631850732
GO:0005516	calmodulin binding	0.0337114631850732
GO:0030594	neurotransmitter receptor activity	0.0337114631850732
GO:0042165	neurotransmitter binding	0.0337114631850732
GO:0045211	postsynaptic membrane	0.0337114631850732
GO:0044456	synapse part	0.0337114631850732
GO:0015276	ligand-gated ion channel activity	0.0337114631850732
GO:0022834	ligand-gated channel activity	0.0337114631850732
GO:0005875	microtubule associated complex	0.0357160778536372
GO:0008509	anion transmembrane transporter activity	0.0400708342034334
GO:0015698	inorganic anion transport	0.0482045333896773

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	5.55e-56	57
neural rod	5.55e-56	57
future spinal cord	5.55e-56	57
neural keel	5.55e-56	57
regional part of nervous system	5.67e-53	94
nervous system	5.67e-53	94
central nervous system	1.62e-52	82
neurectoderm	1.00e-46	90
regional part of brain	1.37e-46	59
regional part of forebrain	1.46e-46	41
forebrain	1.46e-46	41
future forebrain	1.46e-46	41
adult organism	1.60e-46	115
neural plate	1.62e-45	86
presumptive neural plate	1.62e-45	86
brain	3.14e-45	69
future brain	3.14e-45	69
anterior neural tube	4.72e-45	42
gray matter	8.55e-39	34
brain grey matter	8.55e-39	34
telencephalon	1.28e-38	34
regional part of telencephalon	1.65e-37	33
cerebral hemisphere	8.17e-37	32
ectoderm	1.36e-35	173
presumptive ectoderm	1.36e-35	173
pre-chordal neural plate	2.04e-34	61
ectoderm-derived structure	3.20e-34	169
anterior region of body	9.73e-31	129
craniocervical region	9.73e-31	129
head	2.24e-29	123
cerebral cortex	6.04e-29	25
pallium	6.04e-29	25
regional part of cerebral cortex	4.57e-27	22
neocortex	8.06e-25	20
organ part	7.73e-13	219
posterior neural tube	6.91e-12	15
chordal neural plate	6.91e-12	15
basal ganglion	2.58e-11	9
nuclear complex of neuraxis	2.58e-11	9
aggregate regional part of brain	2.58e-11	9
collection of basal ganglia	2.58e-11	9
cerebral subcortex	2.58e-11	9
nucleus of brain	3.63e-11	9
neural nucleus	3.63e-11	9
tube	5.07e-11	194
epithelium	5.66e-11	309
organism subdivision	1.14e-10	365
cell layer	1.32e-10	312
anatomical conduit	1.38e-10	241
temporal lobe	2.64e-10	7
multi-tissue structure	2.92e-10	347
segmental subdivision of nervous system	6.05e-10	13
anatomical cluster	2.21e-09	286
diencephalon	3.38e-09	7
future diencephalon	3.38e-09	7
segmental subdivision of hindbrain	4.36e-09	12
hindbrain	4.36e-09	12
presumptive hindbrain	4.36e-09	12
telencephalic nucleus	4.82e-09	7
embryo	8.11e-09	612
gyrus	1.77e-08	6
organ	7.91e-08	511
brainstem	2.76e-07	8
limbic system	3.54e-07	5
occipital lobe	3.63e-07	5
germ layer	3.87e-07	604
embryonic tissue	3.87e-07	604
presumptive structure	3.87e-07	604
epiblast (generic)	3.87e-07	604
parietal lobe	4.14e-07	5
embryonic structure	4.62e-07	605
developing anatomical structure	4.62e-07	605
multi-cellular organism	7.81e-07	659

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.