Coexpression cluster:C3355

Full id: C3355_cerebellum_Neural_occipital_small_parietal_Neurons_neuroblastoma

Phase1 CAGE Peaks

Hg19::chr13:113656022..113656041,+	p9@MCF2L
Hg19::chr13:113656047..113656064,+	p13@MCF2L
Hg19::chr8:62200509..62200590,+	p1@CLVS1

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:0005089	Rho guanyl-nucleotide exchange factor activity	0.0332038149063935
GO:0035023	regulation of Rho protein signal transduction	0.0332038149063935
GO:0005088	Ras guanyl-nucleotide exchange factor activity	0.0332038149063935
GO:0007266	Rho protein signal transduction	0.0332038149063935
GO:0005085	guanyl-nucleotide exchange factor activity	0.0372071117390792
GO:0046578	regulation of Ras protein signal transduction	0.0372071117390792
GO:0007265	Ras protein signal transduction	0.0372071117390792
GO:0005083	small GTPase regulator activity	0.0372071117390792
GO:0051056	regulation of small GTPase mediated signal transduction	0.0372071117390792
GO:0030695	GTPase regulator activity	0.049452490286118

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	1.82e-07	25

Uber Anatomy

Ontology term	p-value	n
central nervous system	3.90e-58	82
neural tube	2.81e-57	57
neural rod	2.81e-57	57
future spinal cord	2.81e-57	57
neural keel	2.81e-57	57
regional part of nervous system	5.95e-57	94
nervous system	5.95e-57	94
regional part of brain	1.74e-49	59
brain	2.37e-49	69
future brain	2.37e-49	69
neural plate	6.93e-46	86
presumptive neural plate	6.93e-46	86
neurectoderm	2.19e-45	90
adult organism	3.49e-45	115
regional part of forebrain	9.52e-45	41
forebrain	9.52e-45	41
future forebrain	9.52e-45	41
anterior neural tube	2.79e-43	42
telencephalon	5.63e-37	34
gray matter	5.96e-37	34
brain grey matter	5.96e-37	34
regional part of telencephalon	6.56e-36	33
cerebral hemisphere	3.79e-35	32
ectoderm	7.01e-35	173
presumptive ectoderm	7.01e-35	173
pre-chordal neural plate	1.07e-34	61
ectoderm-derived structure	1.23e-34	169
anterior region of body	2.27e-31	129
craniocervical region	2.27e-31	129
head	2.70e-30	123
cerebral cortex	9.63e-28	25
pallium	9.63e-28	25
regional part of cerebral cortex	1.42e-25	22
neocortex	1.62e-23	20
tube	2.22e-15	194
organ part	2.30e-15	219
posterior neural tube	1.40e-14	15
chordal neural plate	1.40e-14	15
epithelium	4.90e-13	309
multi-tissue structure	6.27e-13	347
anatomical conduit	6.38e-13	241
organism subdivision	7.80e-13	365
cell layer	1.28e-12	312
segmental subdivision of nervous system	1.41e-12	13
anatomical cluster	4.57e-12	286
segmental subdivision of hindbrain	7.48e-12	12
hindbrain	7.48e-12	12
presumptive hindbrain	7.48e-12	12
basal ganglion	1.39e-10	9
nuclear complex of neuraxis	1.39e-10	9
aggregate regional part of brain	1.39e-10	9
collection of basal ganglia	1.39e-10	9
cerebral subcortex	1.39e-10	9
embryo	1.39e-10	612
nucleus of brain	1.52e-10	9
neural nucleus	1.52e-10	9
temporal lobe	1.31e-09	7
organ	3.70e-09	511
regional part of metencephalon	4.46e-09	9
metencephalon	4.46e-09	9
future metencephalon	4.46e-09	9
diencephalon	4.79e-09	7
future diencephalon	4.79e-09	7
telencephalic nucleus	1.21e-08	7
germ layer	1.67e-08	604
embryonic tissue	1.67e-08	604
presumptive structure	1.67e-08	604
epiblast (generic)	1.67e-08	604
multi-cellular organism	1.74e-08	659
embryonic structure	2.04e-08	605
developing anatomical structure	2.04e-08	605
gyrus	5.07e-08	6
anatomical system	1.41e-07	625
anatomical group	1.70e-07	626
parietal lobe	5.60e-07	5
brainstem	6.40e-07	8
occipital lobe	7.25e-07	5

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
GATA3#2625	2	18.1576775714707	0.00394454681927962	0.0189417685989583
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.0460248127480545
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109092694967296

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.