Coexpression cluster:C774

Full id: C774_neuroblastoma_optic_medulloblastoma_rhabdomyosarcoma_corpus_thyroid_acute

Phase1 CAGE Peaks

Hg19::chr4:96410648..96410672,-	p@chr4:96410648..96410672 -
Hg19::chr4:96446743..96446748,-	p@chr4:96446743..96446748 -
Hg19::chr4:96454053..96454065,-	p@chr4:96454053..96454065 -
Hg19::chr4:96470108..96470130,-	p1@UNC5C
Hg19::chr4:96470148..96470181,-	p3@UNC5C
Hg19::chr4:96470224..96470247,-	p5@UNC5C
Hg19::chr4:96470248..96470259,-	p6@UNC5C
Hg19::chr4:96470279..96470333,+	p1@BC041657
Hg19::chr4:96470350..96470373,-	p2@UNC5C
Hg19::chr4:96470381..96470386,-	p7@UNC5C
Hg19::chr4:96470495..96470515,+	p2@BC041657

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:0005042	netrin receptor activity	0.00335570469798658
GO:0007411	axon guidance	0.0194351230425056
GO:0030334	regulation of cell migration	0.0194351230425056
GO:0051270	regulation of cell motility	0.0194351230425056
GO:0040012	regulation of locomotion	0.0194351230425056
GO:0040011	locomotion	0.0194351230425056
GO:0007409	axonogenesis	0.0194351230425056
GO:0048667	neuron morphogenesis during differentiation	0.0194351230425056
GO:0048812	neurite morphogenesis	0.0194351230425056
GO:0000904	cellular morphogenesis during differentiation	0.0194351230425056
GO:0031175	neurite development	0.0194351230425056
GO:0007420	brain development	0.0194351230425056
GO:0048666	neuron development	0.0198760970573051
GO:0032990	cell part morphogenesis	0.0203020134228188
GO:0030030	cell projection organization and biogenesis	0.0203020134228188
GO:0048858	cell projection morphogenesis	0.0203020134228188
GO:0030182	neuron differentiation	0.0203020134228188
GO:0016477	cell migration	0.0203020134228188
GO:0007417	central nervous system development	0.0203020134228188
GO:0048699	generation of neurons	0.0203020134228188
GO:0022008	neurogenesis	0.0209332054969639
GO:0051674	localization of cell	0.0279398891158447
GO:0006928	cell motility	0.0279398891158447
GO:0032989	cellular structure morphogenesis	0.0320805369127517
GO:0000902	cell morphogenesis	0.0320805369127517
GO:0007399	nervous system development	0.046205472379969

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
adult organism	1.27e-59	114
neural tube	1.59e-52	56
neural rod	1.59e-52	56
future spinal cord	1.59e-52	56
neural keel	1.59e-52	56
regional part of nervous system	5.68e-49	53
regional part of brain	5.68e-49	53
neural plate	2.58e-46	82
presumptive neural plate	2.58e-46	82
nervous system	4.51e-46	89
brain	6.40e-46	68
future brain	6.40e-46	68
central nervous system	1.44e-45	81
neurectoderm	4.17e-43	86
regional part of forebrain	1.19e-38	41
forebrain	1.19e-38	41
anterior neural tube	1.19e-38	41
future forebrain	1.19e-38	41
structure with developmental contribution from neural crest	6.45e-35	132
telencephalon	4.40e-34	34
brain grey matter	7.74e-34	34
gray matter	7.74e-34	34
ecto-epithelium	4.52e-33	104
pre-chordal neural plate	9.02e-33	61
cerebral hemisphere	1.41e-31	32
regional part of telencephalon	1.48e-31	32
organ system subdivision	1.20e-29	223
regional part of cerebral cortex	5.27e-28	22
ectoderm-derived structure	5.62e-26	171
ectoderm	5.62e-26	171
presumptive ectoderm	5.62e-26	171
neocortex	2.01e-25	20
cerebral cortex	9.90e-24	25
pallium	9.90e-24	25
anatomical cluster	1.83e-22	373
tube	1.44e-14	192
posterior neural tube	1.58e-14	15
chordal neural plate	1.58e-14	15
multi-tissue structure	2.42e-14	342
anatomical conduit	4.21e-14	240
segmental subdivision of nervous system	1.67e-12	13
organ part	9.73e-12	218
basal ganglion	1.27e-11	9
nuclear complex of neuraxis	1.27e-11	9
aggregate regional part of brain	1.27e-11	9
collection of basal ganglia	1.27e-11	9
cerebral subcortex	1.27e-11	9
organ	1.30e-11	503
neural nucleus	1.40e-11	9
nucleus of brain	1.40e-11	9
segmental subdivision of hindbrain	3.09e-11	12
hindbrain	3.09e-11	12
presumptive hindbrain	3.09e-11	12
temporal lobe	1.67e-09	6
telencephalic nucleus	2.34e-09	7
epithelium	1.15e-08	306
embryo	2.14e-08	592
cell layer	2.28e-08	309
regional part of metencephalon	2.46e-08	9
metencephalon	2.46e-08	9
future metencephalon	2.46e-08	9
gyrus	3.21e-08	6
brainstem	4.56e-08	6
developing anatomical structure	5.58e-08	581
embryonic structure	8.02e-08	564
germ layer	1.03e-07	560
germ layer / neural crest	1.03e-07	560
embryonic tissue	1.03e-07	560
presumptive structure	1.03e-07	560
germ layer / neural crest derived structure	1.03e-07	560
epiblast (generic)	1.03e-07	560
limbic system	1.11e-07	5
occipital lobe	2.61e-07	5
parietal lobe	3.12e-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
CTBP2#1488	5	28.5077274269673	4.38027279281381e-07	2.08986436824432e-05
CTCF#10664	8	3.89836827132729	0.000140661176059471	0.00183470870069628
RAD21#5885	8	7.53093374215006	9.5260786570561e-07	4.0690966415717e-05
REST#5978	8	7.01820270263856	1.64058660363651e-06	6.21928218864587e-05
YY1#7528	8	3.57176054534826	0.000268200586690672	0.00286553463666364
ZNF263#10127	8	5.97952119055322	5.60369437973428e-06	0.000168999202230745

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.