Coexpression cluster:C452

Full id: C452_hippocampus_locus_middle_pineal_occipital_thalamus_cerebral

Phase1 CAGE Peaks

Hg19::chr13:36348083..36348094,-	p@chr13:36348083..36348094 -
Hg19::chr13:42896804..42896815,+	p@chr13:42896804..42896815 +
Hg19::chr14:90872343..90872352,+	p20@CALM1
Hg19::chr15:25229566..25229589,+	p3@PAR5
Hg19::chr15:25231001..25231006,+	p@chr15:25231001..25231006 +
Hg19::chr15:25236590..25236600,+	p@chr15:25236590..25236600 +
Hg19::chr15:25241034..25241047,+	p@chr15:25241034..25241047 +
Hg19::chr15:73852545..73852571,-	p@chr15:73852545..73852571 -
Hg19::chr17:44834023..44834067,+	p1@AL049276
Hg19::chr20:4681869..4681942,+	p@chr20:4681869..4681942 +
Hg19::chr2:44546639..44546676,-	p@chr2:44546639..44546676 -
Hg19::chr3:149683046..149683062,-	p@chr3:149683046..149683062 -
Hg19::chr4:114303804..114303820,+	p7@ANK2
Hg19::chr4:15070456..15070467,+	p@chr4:15070456..15070467 +
Hg19::chr5:71503592..71503603,+	p3@BC047027
Hg19::chr5:71503633..71503644,+	p2@BC047027
Hg19::chr5:71503739..71503750,+	p1@BC047027
Hg19::chr5:71504217..71504228,+	p37@MAP1B
Hg19::chr6:158733491..158733502,+	p5@TULP4
Hg19::chr6:29570683..29570694,-	p@chr6:29570683..29570694 -
Hg19::chr6:46190077..46190088,-	p@chr6:46190077..46190088 -
Hg19::chrX:70794147..70794220,+	p4@OGT

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:0007584	response to nutrient	0.0018146241377
GO:0031667	response to nutrient levels	0.0018146241377
GO:0009991	response to extracellular stimulus	0.0018146241377
GO:0005737	cytoplasm	0.0190233746672385
GO:0001578	microtubule bundle formation	0.0302789522840798
GO:0016358	dendrite development	0.0310607224280252
GO:0004176	ATP-dependent peptidase activity	0.0310607224280252
GO:0005829	cytosol	0.0310607224280252
GO:0042221	response to chemical stimulus	0.0310607224280252
GO:0044267	cellular protein metabolic process	0.0310607224280252
GO:0007026	negative regulation of microtubule depolymerization	0.0310607224280252
GO:0031114	regulation of microtubule depolymerization	0.0310607224280252
GO:0044260	cellular macromolecule metabolic process	0.0310607224280252
GO:0009605	response to external stimulus	0.0310607224280252
GO:0031111	negative regulation of microtubule polymerization or depolymerization	0.0310607224280252
GO:0007019	microtubule depolymerization	0.0310607224280252
GO:0019538	protein metabolic process	0.0329272534405792
GO:0031110	regulation of microtubule polymerization or depolymerization	0.0341029829548606
GO:0006493	protein amino acid O-linked glycosylation	0.0341029829548606
GO:0031109	microtubule polymerization or depolymerization	0.0345536204345278
GO:0008375	acetylglucosaminyltransferase activity	0.0451180952332877
GO:0051261	protein depolymerization	0.0451180952332877
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0487683090769321
GO:0044424	intracellular part	0.0494291388539985

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	4.86e-28	57
neural rod	4.86e-28	57
future spinal cord	4.86e-28	57
neural keel	4.86e-28	57
central nervous system	5.86e-28	82
regional part of nervous system	1.70e-27	94
nervous system	1.70e-27	94
brain	3.32e-25	69
future brain	3.32e-25	69
adult organism	7.55e-25	115
anterior neural tube	2.39e-24	42
regional part of forebrain	5.86e-24	41
forebrain	5.86e-24	41
future forebrain	5.86e-24	41
regional part of brain	2.18e-23	59
neurectoderm	7.50e-21	90
gray matter	1.00e-20	34
brain grey matter	1.00e-20	34
telencephalon	3.54e-20	34
neural plate	6.03e-20	86
presumptive neural plate	6.03e-20	86
regional part of telencephalon	1.07e-19	33
cerebral hemisphere	2.37e-19	32
cerebral cortex	2.82e-15	25
pallium	2.82e-15	25
regional part of cerebral cortex	6.05e-15	22
pre-chordal neural plate	4.87e-14	61
neocortex	1.39e-13	20
ectoderm	1.94e-12	173
presumptive ectoderm	1.94e-12	173
ectoderm-derived structure	1.10e-11	169
head	1.63e-10	123
anterior region of body	8.07e-10	129
craniocervical region	8.07e-10	129
nucleus of brain	6.36e-07	9
neural nucleus	6.36e-07	9
basal ganglion	6.79e-07	9
nuclear complex of neuraxis	6.79e-07	9
aggregate regional part of brain	6.79e-07	9
collection of basal ganglia	6.79e-07	9
cerebral subcortex	6.79e-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.