Coexpression cluster:C1804

Full id: C1804_hippocampus_temporal_duodenum_amygdala_brain_merkel_Neurons

Phase1 CAGE Peaks

Hg19::chr18:67068228..67068257,+	p2@DOK6
Hg19::chr22:26779052..26779057,+	p@chr22:26779052..26779057 +
Hg19::chr5:175223625..175223636,+	p15@CPLX2
Hg19::chr8:65492915..65492932,+	p1@BHLHE22
Hg19::chr8:65492973..65492989,+	p5@BHLHE22

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:0002448	mast cell mediated immunity	0.00402637148661542
GO:0043303	mast cell degranulation	0.00402637148661542
GO:0045576	mast cell activation	0.00402637148661542
GO:0043299	leukocyte degranulation	0.00402637148661542
GO:0002444	myeloid leukocyte mediated immunity	0.00402637148661542
GO:0019905	syntaxin binding	0.00642968469553287
GO:0000149	SNARE binding	0.00642968469553287
GO:0005158	insulin receptor binding	0.00642968469553287
GO:0002274	myeloid leukocyte activation	0.00670884107822723
GO:0006904	vesicle docking during exocytosis	0.00708040750904987
GO:0048278	vesicle docking	0.00708040750904987
GO:0022406	membrane docking	0.00708040750904987
GO:0045055	regulated secretory pathway	0.00911365272578224
GO:0006836	neurotransmitter transport	0.011619925588591
GO:0002443	leukocyte mediated immunity	0.011619925588591
GO:0032403	protein complex binding	0.0137733392856842
GO:0002252	immune effector process	0.0137733392856842
GO:0006887	exocytosis	0.0137733392856842
GO:0045321	leukocyte activation	0.0211380868929689
GO:0001775	cell activation	0.0233065056081194
GO:0045045	secretory pathway	0.0254773357295268
GO:0032940	secretion by cell	0.0300697653881253
GO:0046903	secretion	0.0371399017736141

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>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	3.04e-38	115
regional part of nervous system	2.76e-37	94
nervous system	2.76e-37	94
central nervous system	5.91e-37	82
neural tube	2.49e-34	57
neural rod	2.49e-34	57
future spinal cord	2.49e-34	57
neural keel	2.49e-34	57
brain	3.88e-29	69
future brain	3.88e-29	69
regional part of brain	1.42e-27	59
neurectoderm	8.39e-27	90
regional part of forebrain	6.78e-26	41
forebrain	6.78e-26	41
future forebrain	6.78e-26	41
anterior neural tube	7.48e-25	42
neural plate	2.00e-24	86
presumptive neural plate	2.00e-24	86
gray matter	1.73e-21	34
brain grey matter	1.73e-21	34
telencephalon	2.14e-21	34
regional part of telencephalon	1.29e-20	33
cerebral hemisphere	3.79e-20	32
ectoderm	1.55e-19	173
presumptive ectoderm	1.55e-19	173
regional part of cerebral cortex	1.26e-18	22
ectoderm-derived structure	1.04e-17	169
neocortex	8.28e-17	20
pre-chordal neural plate	3.57e-16	61
cerebral cortex	3.31e-15	25
pallium	3.31e-15	25
anterior region of body	1.46e-14	129
craniocervical region	1.46e-14	129
head	3.11e-14	123
posterior neural tube	1.67e-10	15
chordal neural plate	1.67e-10	15
segmental subdivision of nervous system	2.82e-09	13
multi-cellular organism	3.63e-09	659
segmental subdivision of hindbrain	1.34e-08	12
hindbrain	1.34e-08	12
presumptive hindbrain	1.34e-08	12
embryo	4.17e-08	612
basal ganglion	4.82e-08	9
nuclear complex of neuraxis	4.82e-08	9
aggregate regional part of brain	4.82e-08	9
collection of basal ganglia	4.82e-08	9
cerebral subcortex	4.82e-08	9
nucleus of brain	8.06e-08	9
neural nucleus	8.06e-08	9
tube	1.80e-07	194
organ	1.95e-07	511
embryonic structure	2.34e-07	605
developing anatomical structure	2.34e-07	605
germ layer	4.27e-07	604
embryonic tissue	4.27e-07	604
presumptive structure	4.27e-07	604
epiblast (generic)	4.27e-07	604
organism subdivision	9.60e-07	365

Disease

Ontology term	p-value	n
neuroectodermal tumor	6.68e-08	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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
SUZ12#23512	2	20.0463123644252	0.00382407565415475	0.0188735238053149

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.