Coexpression cluster:C2350

Full id: C2350_medial_brain_amygdala_hippocampus_neuroectodermal_occipital_small

Phase1 CAGE Peaks

Hg19::chr15:77907614..77907624,-	p17@LINGO1
Hg19::chr15:77907723..77907735,-	p13@LINGO1
Hg19::chr19:42486186..42486199,-	p6@ATP1A3
Hg19::chr6:110448757..110448782,-	p9@WASF1

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:0035235	ionotropic glutamate receptor signaling pathway	0.0147744428218659
GO:0006928	cell motility	0.0147744428218659
GO:0051674	localization of cell	0.0147744428218659
GO:0008542	visual learning	0.0147744428218659
GO:0005890	sodium:potassium-exchanging ATPase complex	0.0147744428218659
GO:0007632	visual behavior	0.0147744428218659
GO:0007613	memory	0.0147744428218659
GO:0030641	cellular hydrogen ion homeostasis	0.0147744428218659
GO:0008344	adult locomotory behavior	0.0147744428218659
GO:0030004	cellular monovalent inorganic cation homeostasis	0.0147744428218659
GO:0055067	monovalent inorganic cation homeostasis	0.0147744428218659
GO:0005391	sodium:potassium-exchanging ATPase activity	0.0147744428218659
GO:0007612	learning	0.0147744428218659
GO:0030317	sperm motility	0.0158154819779361
GO:0007215	glutamate signaling pathway	0.0158154819779361
GO:0030534	adult behavior	0.0190599366900479
GO:0030041	actin filament polymerization	0.0205939328850991
GO:0007611	learning and/or memory	0.0275956377504917
GO:0008154	actin polymerization and/or depolymerization	0.0355408482650936
GO:0042493	response to drug	0.0355408482650936
GO:0009416	response to light stimulus	0.0434963365107109
GO:0031402	sodium ion binding	0.0474286948824892
GO:0051258	protein polymerization	0.0474286948824892
GO:0009314	response to radiation	0.0474286948824892

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
neurectodermal cell	2.27e-07	59

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	2.48e-31	94
nervous system	2.48e-31	94
central nervous system	4.98e-30	82
neural tube	4.39e-26	57
neural rod	4.39e-26	57
future spinal cord	4.39e-26	57
neural keel	4.39e-26	57
neurectoderm	8.14e-25	90
brain	3.37e-24	69
future brain	3.37e-24	69
gray matter	1.02e-22	34
brain grey matter	1.02e-22	34
telencephalon	1.18e-22	34
regional part of forebrain	1.56e-22	41
forebrain	1.56e-22	41
future forebrain	1.56e-22	41
neural plate	5.21e-22	86
presumptive neural plate	5.21e-22	86
regional part of telencephalon	8.72e-22	33
regional part of brain	1.04e-21	59
anterior neural tube	1.27e-21	42
cerebral hemisphere	1.60e-21	32
ectoderm	4.13e-21	173
presumptive ectoderm	4.13e-21	173
regional part of cerebral cortex	4.56e-19	22
ectoderm-derived structure	7.05e-19	169
cerebral cortex	3.56e-18	25
pallium	3.56e-18	25
neocortex	2.49e-17	20
pre-chordal neural plate	4.60e-17	61
head	1.21e-15	123
anterior region of body	4.76e-15	129
craniocervical region	4.76e-15	129
adult organism	5.68e-14	115
gyrus	7.21e-07	6

Disease

Ontology term	p-value	n
neuroectodermal tumor	6.80e-07	10

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.