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>cell_data<br>uberon_data<br>disease_data<br>

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Cell Type

Ontology term	p-value	n
neuronal stem cell	1.03e-07	8

Uber Anatomy

Ontology term	p-value	n
nervous system	7.98e-81	89
central nervous system	1.53e-75	81
neural tube	5.48e-68	56
neural rod	5.48e-68	56
future spinal cord	5.48e-68	56
neural keel	5.48e-68	56
regional part of nervous system	1.83e-65	53
regional part of brain	1.83e-65	53
brain	5.27e-62	68
future brain	5.27e-62	68
brain grey matter	2.32e-52	34
gray matter	2.32e-52	34
telencephalon	4.52e-52	34
cerebral hemisphere	7.41e-52	32
regional part of forebrain	3.71e-51	41
forebrain	3.71e-51	41
anterior neural tube	3.71e-51	41
future forebrain	3.71e-51	41
neurectoderm	4.82e-51	86
neural plate	2.81e-49	82
presumptive neural plate	2.81e-49	82
regional part of cerebral cortex	2.20e-48	22
regional part of telencephalon	4.87e-48	32
ectoderm-derived structure	1.70e-44	171
ectoderm	1.70e-44	171
presumptive ectoderm	1.70e-44	171
neocortex	1.97e-43	20
adult organism	3.33e-42	114
cerebral cortex	5.33e-42	25
pallium	5.33e-42	25
ecto-epithelium	2.64e-40	104
pre-chordal neural plate	4.91e-38	61
organ system subdivision	3.13e-36	223
structure with developmental contribution from neural crest	1.13e-28	132
posterior neural tube	3.30e-17	15
chordal neural plate	3.30e-17	15
anatomical cluster	6.40e-17	373
segmental subdivision of hindbrain	6.37e-15	12
hindbrain	6.37e-15	12
presumptive hindbrain	6.37e-15	12
gyrus	4.14e-14	6
brainstem	6.00e-14	6
tube	6.40e-14	192
segmental subdivision of nervous system	1.27e-13	13
limbic system	2.39e-13	5
temporal lobe	6.28e-13	6
occipital lobe	7.35e-13	5
parietal lobe	1.59e-12	5
basal ganglion	4.63e-12	9
nuclear complex of neuraxis	4.63e-12	9
aggregate regional part of brain	4.63e-12	9
collection of basal ganglia	4.63e-12	9
cerebral subcortex	4.63e-12	9
neural nucleus	8.93e-12	9
nucleus of brain	8.93e-12	9
organ part	1.76e-11	218
sympathetic nervous system	2.18e-11	5
autonomic nervous system	2.18e-11	5
anatomical conduit	4.41e-10	240
germ layer	1.19e-09	560
germ layer / neural crest	1.19e-09	560
embryonic tissue	1.19e-09	560
presumptive structure	1.19e-09	560
germ layer / neural crest derived structure	1.19e-09	560
epiblast (generic)	1.19e-09	560
embryonic structure	1.90e-09	564
regional part of metencephalon	2.12e-09	9
metencephalon	2.12e-09	9
future metencephalon	2.12e-09	9
embryo	3.13e-09	592
developing anatomical structure	3.65e-09	581
frontal cortex	5.81e-08	3
pons	6.69e-08	3
telencephalic nucleus	7.36e-08	7
medulla oblongata	1.02e-07	3
myelencephalon	1.02e-07	3
future myelencephalon	1.02e-07	3
epithelium	1.54e-07	306
cell layer	2.37e-07	309
multi-tissue structure	3.21e-07	342

Disease

Ontology term	p-value	n
neuroectodermal tumor	2.84e-10	10
neuroendocrine tumor	2.00e-09	6

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.