Coexpression cluster:C599

Full id: C599_medial_neuroectodermal_hippocampus_amygdala_parietal_middle_cerebellum

Phase1 CAGE Peaks

Hg19::chr17:7080883..7080903,-	p6@ASGR1
Hg19::chr19:51162984..51163013,-	p@chr19:51162984..51163013 -
Hg19::chr19:51163812..51163823,-	p@chr19:51163812..51163823 -
Hg19::chr19:51163865..51163880,-	p@chr19:51163865..51163880 -
Hg19::chr19:51164142..51164155,-	p@chr19:51164142..51164155 -
Hg19::chr19:51164317..51164344,-	p@chr19:51164317..51164344 -
Hg19::chr19:51164347..51164387,-	p@chr19:51164347..51164387 -
Hg19::chr19:51164405..51164431,-	p@chr19:51164405..51164431 -
Hg19::chr19:51164492..51164503,-	p@chr19:51164492..51164503 -
Hg19::chr19:51164648..51164677,-	p@chr19:51164648..51164677 -
Hg19::chr19:51164729..51164740,-	p@chr19:51164729..51164740 -
Hg19::chr19:51164762..51164787,-	p@chr19:51164762..51164787 -
Hg19::chr19:51189524..51189535,-	p@chr19:51189524..51189535 -
Hg19::chr19:57159011..57159029,+	p@chr19:57159011..57159029 +
Hg19::chr6:110423382..110423428,-	p4@AK056044

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:0004873	asialoglycoprotein receptor activity	0.00264924055104203
GO:0006898	receptor-mediated endocytosis	0.0181031437654539
GO:0010324	membrane invagination	0.0434916990462734
GO:0006897	endocytosis	0.0434916990462734

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
regional part of nervous system	7.47e-32	94
nervous system	7.47e-32	94
central nervous system	1.62e-29	82
neural tube	2.87e-28	57
neural rod	2.87e-28	57
future spinal cord	2.87e-28	57
neural keel	2.87e-28	57
brain	1.41e-24	69
future brain	1.41e-24	69
regional part of forebrain	2.07e-24	41
forebrain	2.07e-24	41
future forebrain	2.07e-24	41
regional part of brain	6.38e-24	59
neurectoderm	3.09e-23	90
anterior neural tube	3.21e-23	42
neural plate	3.85e-21	86
presumptive neural plate	3.85e-21	86
gray matter	3.00e-20	34
brain grey matter	3.00e-20	34
telencephalon	3.93e-20	34
regional part of telencephalon	1.84e-19	33
cerebral hemisphere	4.26e-19	32
ectoderm	1.34e-17	173
presumptive ectoderm	1.34e-17	173
regional part of cerebral cortex	3.87e-17	22
pre-chordal neural plate	5.08e-16	61
ectoderm-derived structure	5.73e-16	169
neocortex	1.19e-15	20
cerebral cortex	7.40e-15	25
pallium	7.40e-15	25
adult organism	1.69e-12	115
head	4.51e-12	123
anterior region of body	3.50e-11	129
craniocervical region	3.50e-11	129
tube	3.81e-08	194
basal ganglion	5.01e-07	9
nuclear complex of neuraxis	5.01e-07	9
aggregate regional part of brain	5.01e-07	9
collection of basal ganglia	5.01e-07	9
cerebral subcortex	5.01e-07	9
nucleus of brain	7.12e-07	9
neural nucleus	7.12e-07	9

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.