Coexpression cluster:C1759

Full id: C1759_neuroectodermal_neuroblastoma_peripheral_occipital_postcentral_paracentral_parietal

Phase1 CAGE Peaks

Hg19::chr16:25703274..25703350,+	p1@HS3ST4
Hg19::chr8:21645804..21645850,-	p3@GFRA2
Hg19::chr8:21646290..21646308,-	p4@GFRA2
Hg19::chr8:21646311..21646351,-	p1@GFRA2
Hg19::chr8:21646364..21646402,-	p2@GFRA2

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:0016167	glial cell line-derived neurotrophic factor receptor activity	0.00612259915710724
GO:0008467	heparin-glucosamine 3-O-sulfotransferase activity	0.00765291100983854
GO:0030201	heparan sulfate proteoglycan metabolic process	0.0122433959859717
GO:0006029	proteoglycan metabolic process	0.0221856018006757
GO:0008146	sulfotransferase activity	0.0301459095476488
GO:0016782	transferase activity, transferring sulfur-containing groups	0.0301459095476488
GO:0004896	hematopoietin/interferon-class (D200-domain) cytokine receptor activity	0.0301459095476488
GO:0006790	sulfur metabolic process	0.0328682829093709
GO:0019898	extrinsic to membrane	0.0363392028844498
GO:0048503	GPI anchor binding	0.038501975748613

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>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	6.58e-63	114
neural tube	4.91e-41	56
neural rod	4.91e-41	56
future spinal cord	4.91e-41	56
neural keel	4.91e-41	56
nervous system	4.25e-39	89
neurectoderm	3.07e-38	86
regional part of nervous system	1.39e-37	53
regional part of brain	1.39e-37	53
central nervous system	1.46e-37	81
neural plate	3.48e-33	82
presumptive neural plate	3.48e-33	82
brain grey matter	5.77e-32	34
gray matter	5.77e-32	34
telencephalon	5.99e-32	34
regional part of cerebral cortex	1.56e-31	22
brain	4.81e-31	68
future brain	4.81e-31	68
regional part of forebrain	2.34e-30	41
forebrain	2.34e-30	41
anterior neural tube	2.34e-30	41
future forebrain	2.34e-30	41
cerebral hemisphere	6.15e-30	32
regional part of telencephalon	1.77e-29	32
neocortex	5.66e-29	20
cerebral cortex	6.03e-27	25
pallium	6.03e-27	25
ectoderm-derived structure	5.12e-25	171
ectoderm	5.12e-25	171
presumptive ectoderm	5.12e-25	171
ecto-epithelium	5.60e-24	104
pre-chordal neural plate	9.30e-24	61
structure with developmental contribution from neural crest	1.93e-23	132
organ system subdivision	9.74e-23	223
anatomical cluster	3.73e-16	373
embryo	1.93e-15	592
developing anatomical structure	8.13e-13	581
multi-cellular organism	3.58e-12	656
embryonic structure	4.14e-12	564
germ layer	7.33e-12	560
germ layer / neural crest	7.33e-12	560
embryonic tissue	7.33e-12	560
presumptive structure	7.33e-12	560
germ layer / neural crest derived structure	7.33e-12	560
epiblast (generic)	7.33e-12	560
posterior neural tube	1.42e-11	15
chordal neural plate	1.42e-11	15
gyrus	1.29e-10	6
organ	3.22e-10	503
multi-tissue structure	1.57e-09	342
organ part	1.63e-09	218
occipital lobe	3.36e-09	5
parietal lobe	4.62e-09	5
brainstem	6.20e-09	6
tube	7.97e-09	192
segmental subdivision of hindbrain	2.28e-08	12
hindbrain	2.28e-08	12
presumptive hindbrain	2.28e-08	12
temporal lobe	2.50e-08	6
limbic system	3.67e-08	5
anatomical system	7.84e-08	624
anatomical group	9.07e-08	625
segmental subdivision of nervous system	1.44e-07	13
anatomical conduit	4.24e-07	240
basal ganglion	7.89e-07	9
nuclear complex of neuraxis	7.89e-07	9
aggregate regional part of brain	7.89e-07	9
collection of basal ganglia	7.89e-07	9
cerebral subcortex	7.89e-07	9
neural nucleus	9.63e-07	9
nucleus of brain	9.63e-07	9

Disease

Ontology term	p-value	n
neuroectodermal tumor	2.97e-10	10

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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No analysis results for this cluster

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.