Coexpression cluster:C1654

Full id: C1654_smallcell_cord_small_B_Neural_gastrointestinal_splenic

Phase1 CAGE Peaks

Hg19::chr12:103351813..103351844,+	p4@ASCL1
Hg19::chr12:103352277..103352324,+	p2@ASCL1
Hg19::chr12:103352326..103352351,+	p3@ASCL1
Hg19::chr12:103352595..103352622,+	p@chr12:103352595..103352622 +
Hg19::chr3:179754677..179754701,-	p5@PEX5L

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:0060163	subpallium neuron fate commitment	0.000804584167353507
GO:0014017	neuroblast fate commitment	0.000804584167353507
GO:0014016	neuroblast differentiation	0.000804584167353507
GO:0007400	neuroblast fate determination	0.000804584167353507
GO:0060165	regulation of timing of subpallium neuron differentiation	0.000804584167353507
GO:0060164	regulation of timing of neuron differentiation	0.000804584167353507
GO:0021544	subpallium development	0.00206886981320192
GO:0048505	regulation of timing of cell differentiation	0.00214546304184275
GO:0040034	regulation of development, heterochronic	0.00214546304184275
GO:0021537	telencephalon development	0.00530947391795865
GO:0048663	neuron fate commitment	0.00614292166841388
GO:0007405	neuroblast proliferation	0.0068373548804725
GO:0045664	regulation of neuron differentiation	0.00932932998797643
GO:0010001	glial cell differentiation	0.00932932998797643
GO:0001709	cell fate determination	0.00932932998797643
GO:0042063	gliogenesis	0.0102176854681714
GO:0001764	neuron migration	0.0102176854681714
GO:0030900	forebrain development	0.0123287861003839
GO:0007219	Notch signaling pathway	0.0126947983978901
GO:0045165	cell fate commitment	0.0171199860133783
GO:0007389	pattern specification process	0.0284536626285139
GO:0007420	brain development	0.0301607648054761
GO:0045595	regulation of cell differentiation	0.0301607648054761
GO:0048666	neuron development	0.0309067338413351
GO:0030182	neuron differentiation	0.0401418013441119
GO:0016477	cell migration	0.0401418013441119
GO:0007417	central nervous system development	0.0401418013441119
GO:0050793	regulation of developmental process	0.0401418013441119
GO:0048699	generation of neurons	0.0401418013441119
GO:0022008	neurogenesis	0.0419982514204205

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	1.13e-86	56
neural rod	1.13e-86	56
future spinal cord	1.13e-86	56
neural keel	1.13e-86	56
nervous system	1.88e-80	89
regional part of nervous system	3.02e-80	53
regional part of brain	3.02e-80	53
central nervous system	8.76e-78	81
regional part of forebrain	5.79e-71	41
forebrain	5.79e-71	41
anterior neural tube	5.79e-71	41
future forebrain	5.79e-71	41
brain grey matter	3.99e-65	34
gray matter	3.99e-65	34
brain	4.06e-65	68
future brain	4.06e-65	68
telencephalon	5.92e-65	34
cerebral hemisphere	3.43e-61	32
regional part of telencephalon	7.38e-61	32
neural plate	3.10e-60	82
presumptive neural plate	3.10e-60	82
neurectoderm	8.48e-57	86
pre-chordal neural plate	1.08e-49	61
cerebral cortex	7.85e-48	25
pallium	7.85e-48	25
regional part of cerebral cortex	1.06e-46	22
ecto-epithelium	1.53e-46	104
neocortex	3.22e-42	20
ectoderm-derived structure	1.21e-37	171
ectoderm	1.21e-37	171
presumptive ectoderm	1.21e-37	171
adult organism	3.23e-36	114
structure with developmental contribution from neural crest	2.16e-35	132
organ system subdivision	3.78e-35	223
tube	4.05e-20	192
neural nucleus	2.54e-18	9
nucleus of brain	2.54e-18	9
basal ganglion	2.66e-18	9
nuclear complex of neuraxis	2.66e-18	9
aggregate regional part of brain	2.66e-18	9
collection of basal ganglia	2.66e-18	9
cerebral subcortex	2.66e-18	9
posterior neural tube	1.34e-16	15
chordal neural plate	1.34e-16	15
anatomical cluster	1.47e-15	373
gyrus	1.96e-14	6
telencephalic nucleus	3.11e-14	7
brainstem	5.22e-14	6
organ part	2.02e-13	218
anatomical conduit	2.15e-13	240
segmental subdivision of nervous system	6.43e-13	13
occipital lobe	1.62e-12	5
parietal lobe	2.16e-12	5
temporal lobe	3.57e-12	6
limbic system	3.80e-12	5
segmental subdivision of hindbrain	3.65e-11	12
hindbrain	3.65e-11	12
presumptive hindbrain	3.65e-11	12
epithelium	1.29e-10	306
cell layer	2.22e-10	309
corpus striatum	6.08e-09	4
striatum	6.08e-09	4
ventral part of telencephalon	6.08e-09	4
future corpus striatum	6.08e-09	4
multi-tissue structure	1.41e-08	342
frontal cortex	2.90e-08	3
medulla oblongata	5.41e-08	3
myelencephalon	5.41e-08	3
future myelencephalon	5.41e-08	3
diencephalon	5.74e-08	7
future diencephalon	5.74e-08	7
spinal cord	9.08e-08	3
dorsal region element	9.08e-08	3
dorsum	9.08e-08	3
pons	1.09e-07	3
germ layer	3.38e-07	560
germ layer / neural crest	3.38e-07	560
embryonic tissue	3.38e-07	560
presumptive structure	3.38e-07	560
germ layer / neural crest derived structure	3.38e-07	560
epiblast (generic)	3.38e-07	560
embryonic structure	5.09e-07	564
caudate-putamen	5.79e-07	3
dorsal striatum	5.79e-07	3
developing anatomical structure	9.57e-07	581

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
CTCF#10664	4	4.28820509846002	0.00515201558824328	0.0239227883701111
SUZ12#23512	3	30.0694685466377	7.70283100694034e-05	0.00118811987525305

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.