Coexpression cluster:C729

Full id: C729_diencephalon_corpus_thalamus_occipital_brain_medulla_frontal

Phase1 CAGE Peaks

Hg19::chr10:98104208..98104212,-	p@chr10:98104208..98104212 -
Hg19::chr10:98119004..98119021,-	p6@OPALIN
Hg19::chr14:91199850..91199861,-	p@chr14:91199850..91199861 -
Hg19::chr15:29362934..29362952,+	p12@APBA2
Hg19::chr17:40120071..40120085,+	p15@CNP
Hg19::chr1:102830819..102830832,-	p@chr1:102830819..102830832 -
Hg19::chr5:161277768..161277782,+	p8@GABRA1
Hg19::chr6:154589029..154589034,-	p@chr6:154589029..154589034 -
Hg19::chr7:124391226..124391235,-	p@chr7:124391226..124391235 -
Hg19::chr8:27336724..27336740,-	p2@CHRNA2
Hg19::chr8:27336747..27336786,-	p1@CHRNA2

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:0005230	extracellular ligand-gated ion channel activity	0.00218984226483319
GO:0030594	neurotransmitter receptor activity	0.00218984226483319
GO:0042165	neurotransmitter binding	0.00218984226483319
GO:0045211	postsynaptic membrane	0.00218984226483319
GO:0044456	synapse part	0.00218984226483319
GO:0015276	ligand-gated ion channel activity	0.00218984226483319
GO:0022834	ligand-gated channel activity	0.00218984226483319
GO:0004113	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity	0.00290422436151884
GO:0009214	cyclic nucleotide catabolic process	0.00290422436151884
GO:0030054	cell junction	0.0104193408310402
GO:0022836	gated channel activity	0.0130906880856879
GO:0005892	nicotinic acetylcholine-gated receptor-channel complex	0.0141512183731324
GO:0005216	ion channel activity	0.0158057161306655
GO:0022838	substrate specific channel activity	0.0158057161306655
GO:0022803	passive transmembrane transporter activity	0.0158057161306655
GO:0015267	channel activity	0.0158057161306655
GO:0015464	acetylcholine receptor activity	0.0158057161306655
GO:0042166	acetylcholine binding	0.0158057161306655
GO:0004889	nicotinic acetylcholine-activated cation-selective channel activity	0.0158057161306655
GO:0009166	nucleotide catabolic process	0.0161635391315681
GO:0007214	gamma-aminobutyric acid signaling pathway	0.0161635391315681
GO:0004890	GABA-A receptor activity	0.0231299660486301
GO:0043176	amine binding	0.0245209602058705
GO:0016917	GABA receptor activity	0.0245209602058705
GO:0004112	cyclic-nucleotide phosphodiesterase activity	0.0245209602058705
GO:0009187	cyclic nucleotide metabolic process	0.025079492031823
GO:0006810	transport	0.0250847393240961
GO:0051234	establishment of localization	0.0259695966312425
GO:0043168	anion binding	0.0260711541028255
GO:0031404	chloride ion binding	0.0260711541028255
GO:0051179	localization	0.0277142115861157
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.0277142115861157
GO:0015075	ion transmembrane transporter activity	0.0277142115861157
GO:0005887	integral to plasma membrane	0.0277142115861157
GO:0031226	intrinsic to plasma membrane	0.0277142115861157
GO:0006811	ion transport	0.0277142115861157
GO:0005254	chloride channel activity	0.0277142115861157
GO:0048770	pigment granule	0.0277142115861157
GO:0042470	melanosome	0.0277142115861157
GO:0006821	chloride transport	0.0283185860774372
GO:0022891	substrate-specific transmembrane transporter activity	0.0306335778602095
GO:0005253	anion channel activity	0.0309822963045119
GO:0043235	receptor complex	0.0328343825739733
GO:0022857	transmembrane transporter activity	0.0328343825739733
GO:0022892	substrate-specific transporter activity	0.0371058061679059
GO:0007154	cell communication	0.0371058061679059
GO:0008081	phosphoric diester hydrolase activity	0.0381430120006649
GO:0004888	transmembrane receptor activity	0.045364967461019

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
conventional dendritic cell	2.06e-07	8

Uber Anatomy

Ontology term	p-value	n
neural tube	7.06e-32	57
neural rod	7.06e-32	57
future spinal cord	7.06e-32	57
neural keel	7.06e-32	57
central nervous system	1.02e-29	82
regional part of nervous system	2.97e-27	94
nervous system	2.97e-27	94
adult organism	3.62e-27	115
regional part of brain	1.59e-26	59
brain	2.54e-26	69
future brain	2.54e-26	69
regional part of forebrain	9.72e-24	41
forebrain	9.72e-24	41
future forebrain	9.72e-24	41
telencephalon	1.61e-23	34
gray matter	2.08e-23	34
brain grey matter	2.08e-23	34
anterior neural tube	8.01e-23	42
regional part of telencephalon	1.48e-22	33
cerebral hemisphere	1.22e-21	32
neural plate	9.30e-20	86
presumptive neural plate	9.30e-20	86
neurectoderm	5.76e-18	90
regional part of cerebral cortex	1.36e-17	22
neocortex	3.93e-16	20
cerebral cortex	1.33e-15	25
pallium	1.33e-15	25
pre-chordal neural plate	6.98e-15	61
anterior region of body	2.47e-12	129
craniocervical region	2.47e-12	129
head	1.01e-11	123
ectoderm-derived structure	2.37e-10	169
posterior neural tube	3.85e-10	15
chordal neural plate	3.85e-10	15
ectoderm	1.29e-09	173
presumptive ectoderm	1.29e-09	173
nucleus of brain	1.56e-09	9
neural nucleus	1.56e-09	9
basal ganglion	2.41e-09	9
nuclear complex of neuraxis	2.41e-09	9
aggregate regional part of brain	2.41e-09	9
collection of basal ganglia	2.41e-09	9
cerebral subcortex	2.41e-09	9
tube	1.59e-08	194
segmental subdivision of hindbrain	8.84e-08	12
hindbrain	8.84e-08	12
presumptive hindbrain	8.84e-08	12
telencephalic nucleus	1.14e-07	7
gyrus	3.12e-07	6
segmental subdivision of nervous system	6.48e-07	13

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.