Coexpression cluster:C1259

Full id: C1259_Neurons_parietal_occipital_temporal_brain_duodenum_glioblastoma

Phase1 CAGE Peaks

Hg19::chr20:62009349..62009358,-	p10@CHRNA4
Hg19::chr2:104423528..104423529,-	p@chr2:104423528..104423529 -
Hg19::chr4:176734316..176734327,-	p25@GPM6A
Hg19::chr4:176734368..176734405,-	p19@GPM6A
Hg19::chr9:100199546..100199572,-	p@chr9:100199546..100199572 -
Hg19::chr9:100199913..100199937,-	p@chr9:100199913..100199937 -
Hg19::chr9:100199938..100199951,-	p@chr9:100199938..100199951 -

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:0035094	response to nicotine	0.0116780462456223
GO:0043279	response to alkaloid	0.0116780462456223
GO:0014070	response to organic cyclic substance	0.0116780462456223
GO:0005892	nicotinic acetylcholine-gated receptor-channel complex	0.0116780462456223
GO:0015464	acetylcholine receptor activity	0.0116780462456223
GO:0042166	acetylcholine binding	0.0116780462456223
GO:0004889	nicotinic acetylcholine-activated cation-selective channel activity	0.0116780462456223
GO:0005887	integral to plasma membrane	0.0116780462456223
GO:0031226	intrinsic to plasma membrane	0.0116780462456223
GO:0043176	amine binding	0.0172001288703765
GO:0001666	response to hypoxia	0.0172001288703765
GO:0010033	response to organic substance	0.0203612309968446
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.0216421112045033
GO:0044459	plasma membrane part	0.0216421112045033
GO:0043235	receptor complex	0.0280579879925454
GO:0005230	extracellular ligand-gated ion channel activity	0.0280579879925454
GO:0030594	neurotransmitter receptor activity	0.0280579879925454
GO:0042165	neurotransmitter binding	0.0280579879925454
GO:0009986	cell surface	0.0280579879925454
GO:0045211	postsynaptic membrane	0.0280579879925454
GO:0044456	synapse part	0.0280579879925454
GO:0015276	ligand-gated ion channel activity	0.0280579879925454
GO:0022834	ligand-gated channel activity	0.0280579879925454
GO:0005886	plasma membrane	0.0352157565233113
GO:0007268	synaptic transmission	0.0455607017688047
GO:0019226	transmission of nerve impulse	0.0498214260109094

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
neuronal stem cell	2.07e-08	8
neural cell	1.01e-07	25

Uber Anatomy

Ontology term	p-value	n
central nervous system	1.22e-55	82
regional part of nervous system	6.86e-51	94
nervous system	6.86e-51	94
telencephalon	1.61e-47	34
gray matter	1.64e-47	34
brain grey matter	1.64e-47	34
cerebral hemisphere	2.43e-47	32
regional part of forebrain	3.07e-47	41
forebrain	3.07e-47	41
future forebrain	3.07e-47	41
brain	3.72e-47	69
future brain	3.72e-47	69
regional part of cerebral cortex	5.48e-46	22
anterior neural tube	6.31e-46	42
regional part of telencephalon	3.05e-45	33
neural tube	2.62e-44	57
neural rod	2.62e-44	57
future spinal cord	2.62e-44	57
neural keel	2.62e-44	57
cerebral cortex	5.83e-44	25
pallium	5.83e-44	25
regional part of brain	1.76e-42	59
neocortex	1.89e-41	20
neural plate	1.65e-31	86
presumptive neural plate	1.65e-31	86
neurectoderm	1.22e-29	90
pre-chordal neural plate	4.47e-29	61
adult organism	1.36e-26	115
ectoderm-derived structure	1.91e-26	169
ectoderm	1.60e-25	173
presumptive ectoderm	1.60e-25	173
head	2.89e-23	123
anterior region of body	5.85e-23	129
craniocervical region	5.85e-23	129
gyrus	5.20e-16	6
temporal lobe	9.22e-16	7
parietal lobe	1.67e-13	5
tube	1.74e-10	194
middle temporal gyrus	7.30e-09	3
occipital lobe	1.55e-08	5
limbic system	1.55e-08	5
pons	1.19e-07	3

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.