Coexpression cluster:C458

Full id: C458_salivary_parietal_middle_locus_medial_occipital_globus

Phase1 CAGE Peaks

Hg19::chr10:105796014..105796053,-	p@chr10:105796014..105796053 -
Hg19::chr12:52912957..52912973,-	p17@KRT5
Hg19::chr12:52913230..52913233,-	p11@KRT5
Hg19::chr13:43059605..43059611,+	p@chr13:43059605..43059611 +
Hg19::chr1:209741112..209741127,-	p1@ENST00000424696
Hg19::chr1:209741162..209741173,-	p2@ENST00000424696
Hg19::chr20:3295706..3295717,-	p@chr20:3295706..3295717 -
Hg19::chr20:3295742..3295749,-	p@chr20:3295742..3295749 -
Hg19::chr3:48471830..48471839,-	p27@PLXNB1
Hg19::chr5:110104185..110104192,-	p@chr5:110104185..110104192 -
Hg19::chr5:66942627..66942643,-	p1@ENST00000507298
Hg19::chr6:25004699..25004706,-	p@chr6:25004699..25004706 -
Hg19::chr6:25004760..25004769,-	p@chr6:25004760..25004769 -
Hg19::chr6:25004775..25004790,-	p@chr6:25004775..25004790 -
Hg19::chr6:25004791..25004799,-	p@chr6:25004791..25004799 -
Hg19::chr6:25004888..25004899,-	p@chr6:25004888..25004899 -
Hg19::chr6:56488575..56488587,-	p@chr6:56488575..56488587 -
Hg19::chr6:56489323..56489336,-	p@chr6:56489323..56489336 -
Hg19::chrM:294..305,+	p@chrM:294..305 +
Hg19::chrM:313..339,+	p@chrM:313..339 +
Hg19::chrM:408..427,+	p@chrM:408..427 +

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:0030215	semaphorin receptor binding	0.00441540091840339
GO:0017154	semaphorin receptor activity	0.00662290641421346
GO:0050772	positive regulation of axonogenesis	0.0176577044057807
GO:0050769	positive regulation of neurogenesis	0.0176577044057807
GO:0050770	regulation of axonogenesis	0.0229516363620597
GO:0048731	system development	0.0239562660080635
GO:0050767	regulation of neurogenesis	0.0239562660080635
GO:0048856	anatomical structure development	0.0326402836208885
GO:0051094	positive regulation of developmental process	0.0333279086719243
GO:0007275	multicellular organismal development	0.0340768241083792
GO:0005200	structural constituent of cytoskeleton	0.0340768241083792
GO:0007409	axonogenesis	0.0349943232195785
GO:0048667	neuron morphogenesis during differentiation	0.0349943232195785
GO:0048812	neurite morphogenesis	0.0349943232195785
GO:0000904	cellular morphogenesis during differentiation	0.0349943232195785
GO:0031175	neurite development	0.0349943232195785
GO:0008544	epidermis development	0.0349943232195785
GO:0007398	ectoderm development	0.0354912267981477
GO:0048666	neuron development	0.0354912267981477
GO:0032502	developmental process	0.0354912267981477
GO:0032990	cell part morphogenesis	0.0354912267981477
GO:0030030	cell projection organization and biogenesis	0.0354912267981477
GO:0048858	cell projection morphogenesis	0.0354912267981477
GO:0030182	neuron differentiation	0.0354912267981477
GO:0032501	multicellular organismal process	0.0354912267981477
GO:0016477	cell migration	0.0354912267981477
GO:0050793	regulation of developmental process	0.0354912267981477
GO:0005882	intermediate filament	0.0354912267981477
GO:0045111	intermediate filament cytoskeleton	0.0354912267981477
GO:0048699	generation of neurons	0.0354912267981477
GO:0022008	neurogenesis	0.0371739046797585
GO:0009888	tissue development	0.0418959878611011
GO:0051674	localization of cell	0.0494585425614447
GO:0006928	cell motility	0.0494585425614447

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
adult organism	6.63e-22	115
neural tube	6.20e-16	57
neural rod	6.20e-16	57
future spinal cord	6.20e-16	57
neural keel	6.20e-16	57
central nervous system	5.07e-14	82
regional part of nervous system	3.37e-13	94
nervous system	3.37e-13	94
regional part of forebrain	7.80e-13	41
forebrain	7.80e-13	41
future forebrain	7.80e-13	41
anterior neural tube	8.48e-13	42
brain	4.65e-12	69
future brain	4.65e-12	69
regional part of brain	8.09e-12	59
gray matter	6.52e-11	34
brain grey matter	6.52e-11	34
neurectoderm	8.83e-11	90
neural plate	3.73e-10	86
presumptive neural plate	3.73e-10	86
ectoderm	4.86e-10	173
presumptive ectoderm	4.86e-10	173
regional part of telencephalon	8.35e-10	33
telencephalon	1.06e-09	34
ectoderm-derived structure	1.80e-09	169
cerebral hemisphere	3.59e-09	32
anterior region of body	8.30e-08	129
craniocervical region	8.30e-08	129
regional part of cerebral cortex	9.88e-08	22
head	1.90e-07	123
cerebral cortex	9.81e-07	25
pallium	9.81e-07	25

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
STAT3#6774	8	4.00741523701114	0.000434040818520202	0.00405173302157949

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.