Coexpression cluster:C919

Full id: C919_Neurons_Neural_parietal_Astrocyte_duodenum_occipital_temporal

Phase1 CAGE Peaks

Hg19::chr17:49124024..49124036,-	p10@SPAG9
Hg19::chr2:105467904..105467924,-	p1@ENST00000413121 p1@ENST00000443988 p1@ENST00000458253 p1@uc002tck.1
Hg19::chr2:105470562..105470582,+	p5@POU3F3
Hg19::chr2:105470599..105470610,+	p6@POU3F3
Hg19::chr6:123101428..123101450,+	p@chr6:123101428..123101450 +
Hg19::chr6:98264524..98264558,+	p@chr6:98264524..98264558 +
Hg19::chr6:99282570..99282591,+	p4@POU3F2
Hg19::chr6:99282592..99282616,+	p3@POU3F2
Hg19::chr6:99283040..99283063,+	p5@POU3F2

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:0021985	neurohypophysis development	0.00635789657521692
GO:0021979	hypothalamus cell differentiation	0.00635789657521692
GO:0021854	hypothalamus development	0.00635789657521692
GO:0014002	astrocyte development	0.00635789657521692
GO:0021761	limbic system development	0.00826417063337453
GO:0048708	astrocyte differentiation	0.00826417063337453
GO:0021983	pituitary gland development	0.00826417063337453
GO:0040018	positive regulation of multicellular organism growth	0.00826417063337453
GO:0021536	diencephalon development	0.00826417063337453
GO:0021782	glial cell development	0.00826417063337453
GO:0040014	regulation of multicellular organism growth	0.0108960427314122
GO:0045927	positive regulation of growth	0.0108960427314122
GO:0035264	multicellular organism growth	0.0108960427314122
GO:0001669	acrosome	0.0108960427314122
GO:0050770	regulation of axonogenesis	0.0110167854537886
GO:0010001	glial cell differentiation	0.0115194470888124
GO:0035270	endocrine system development	0.0123365310940337
GO:0042063	gliogenesis	0.0127094295453305
GO:0050767	regulation of neurogenesis	0.0127094295453305
GO:0030900	forebrain development	0.0139182114861477
GO:0048732	gland development	0.0139182114861477
GO:0007409	axonogenesis	0.0308770916361527
GO:0048667	neuron morphogenesis during differentiation	0.0308770916361527
GO:0048812	neurite morphogenesis	0.0308770916361527
GO:0000904	cellular morphogenesis during differentiation	0.0308770916361527
GO:0031175	neurite development	0.0308770916361527
GO:0008544	epidermis development	0.0308770916361527
GO:0007420	brain development	0.0308770916361527
GO:0045595	regulation of cell differentiation	0.0308770916361527
GO:0007398	ectoderm development	0.0308770916361527
GO:0048666	neuron development	0.0315146554353818
GO:0005764	lysosome	0.0335936865800335
GO:0040008	regulation of growth	0.0335936865800335
GO:0000323	lytic vacuole	0.0335936865800335
GO:0032990	cell part morphogenesis	0.0335936865800335
GO:0030030	cell projection organization and biogenesis	0.0335936865800335
GO:0048858	cell projection morphogenesis	0.0335936865800335
GO:0030182	neuron differentiation	0.0335936865800335
GO:0007283	spermatogenesis	0.0335936865800335
GO:0048232	male gamete generation	0.0335936865800335
GO:0005773	vacuole	0.0339849946966792
GO:0008284	positive regulation of cell proliferation	0.0339849946966792
GO:0007417	central nervous system development	0.0339849946966792
GO:0050793	regulation of developmental process	0.0339849946966792
GO:0048699	generation of neurons	0.0340715777262218
GO:0022008	neurogenesis	0.0355757701702134
GO:0007276	gamete generation	0.0355757701702134
GO:0009888	tissue development	0.040220148346657
GO:0019953	sexual reproduction	0.040685094257863
GO:0042802	identical protein binding	0.0460402262403028

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><br>

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Cell Type

Ontology term	p-value	n
neural cell	1.31e-11	25
astrocyte of the cerebral cortex	2.85e-09	3
oligodendrocyte	3.52e-09	7
macroglial cell	3.52e-09	7
astrocyte	3.52e-09	7
oligodendrocyte precursor cell	3.52e-09	7
neuronal stem cell	5.99e-09	8
neurectodermal cell	7.78e-07	59

Uber Anatomy

Ontology term	p-value	n
neural tube	4.47e-101	56
neural rod	4.47e-101	56
future spinal cord	4.47e-101	56
neural keel	4.47e-101	56
central nervous system	3.30e-99	81
nervous system	6.43e-98	89
regional part of nervous system	1.75e-94	53
regional part of brain	1.75e-94	53
brain	2.25e-80	68
future brain	2.25e-80	68
neurectoderm	3.67e-78	86
regional part of forebrain	1.56e-76	41
forebrain	1.56e-76	41
anterior neural tube	1.56e-76	41
future forebrain	1.56e-76	41
telencephalon	3.60e-74	34
neural plate	9.47e-74	82
presumptive neural plate	9.47e-74	82
brain grey matter	1.74e-73	34
gray matter	1.74e-73	34
cerebral hemisphere	2.22e-69	32
regional part of telencephalon	3.96e-69	32
ecto-epithelium	4.87e-60	104
pre-chordal neural plate	6.39e-57	61
ectoderm-derived structure	2.30e-56	171
ectoderm	2.30e-56	171
presumptive ectoderm	2.30e-56	171
cerebral cortex	3.87e-53	25
pallium	3.87e-53	25
regional part of cerebral cortex	1.67e-45	22
structure with developmental contribution from neural crest	3.14e-44	132
neocortex	5.93e-41	20
adult organism	1.05e-36	114
organ system subdivision	2.06e-35	223
posterior neural tube	2.95e-24	15
chordal neural plate	2.95e-24	15
basal ganglion	1.17e-21	9
nuclear complex of neuraxis	1.17e-21	9
aggregate regional part of brain	1.17e-21	9
collection of basal ganglia	1.17e-21	9
cerebral subcortex	1.17e-21	9
neural nucleus	2.71e-21	9
nucleus of brain	2.71e-21	9
tube	3.38e-21	192
segmental subdivision of nervous system	1.32e-20	13
segmental subdivision of hindbrain	2.77e-18	12
hindbrain	2.77e-18	12
presumptive hindbrain	2.77e-18	12
anatomical cluster	9.27e-18	373
telencephalic nucleus	3.81e-17	7
gyrus	1.79e-15	6
brainstem	1.28e-14	6
anatomical conduit	2.40e-14	240
temporal lobe	2.38e-13	6
limbic system	4.00e-13	5
parietal lobe	4.65e-13	5
organ part	1.59e-12	218
regional part of metencephalon	5.05e-12	9
metencephalon	5.05e-12	9
future metencephalon	5.05e-12	9
epithelium	8.76e-12	306
cell layer	1.54e-11	309
corpus striatum	1.37e-10	4
striatum	1.37e-10	4
ventral part of telencephalon	1.37e-10	4
future corpus striatum	1.37e-10	4
multi-tissue structure	4.44e-09	342
occipital lobe	7.52e-09	5
frontal cortex	1.27e-08	3
embryo	1.62e-08	592
medulla oblongata	2.57e-08	3
myelencephalon	2.57e-08	3
future myelencephalon	2.57e-08	3
caudate-putamen	3.65e-08	3
dorsal striatum	3.65e-08	3
pons	5.54e-08	3
developing anatomical structure	6.74e-08	581
germ layer	8.77e-08	560
germ layer / neural crest	8.77e-08	560
embryonic tissue	8.77e-08	560
presumptive structure	8.77e-08	560
germ layer / neural crest derived structure	8.77e-08	560
epiblast (generic)	8.77e-08	560
spinal cord	9.01e-08	3
dorsal region element	9.01e-08	3
dorsum	9.01e-08	3
embryonic structure	1.31e-07	564

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
CTBP2#1488	2	13.9371111865174	0.00849282348620567	0.0324248580543167
NANOG#79923	3	9.74825949367088	0.00287455368798437	0.0155721516997458
SUZ12#23512	3	16.7052603036876	0.000609326676846205	0.00508530196604929

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.