Coexpression cluster:C1472

Full id: C1472_nonsmall_neuroblastoma_small_tubular_carcinoid_smallcell_merkel

Phase1 CAGE Peaks

Hg19::chr1:235813008..235813019,-	p8@GNG4
Hg19::chr1:235813034..235813097,-	p1@GNG4
Hg19::chr1:235813117..235813120,-	p11@GNG4
Hg19::chr1:235813272..235813285,-	p6@GNG4
Hg19::chr1:235813290..235813323,-	p2@GNG4
Hg19::chr1:235813325..235813360,-	p3@GNG4

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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No GOStat results

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
neural cell	3.78e-13	25
neuronal stem cell	9.50e-09	8
neuron	3.70e-07	6
neuroblast	3.70e-07	6
electrically signaling cell	3.70e-07	6
neurectodermal cell	5.41e-07	59
neuron associated cell	6.64e-07	17
neuron associated cell (sensu Vertebrata)	6.64e-07	17

Uber Anatomy

Ontology term	p-value	n
nervous system	1.32e-37	89
central nervous system	1.65e-36	81
neural tube	6.38e-27	56
neural rod	6.38e-27	56
future spinal cord	6.38e-27	56
neural keel	6.38e-27	56
organ system subdivision	6.61e-27	223
brain	7.53e-27	68
future brain	7.53e-27	68
regional part of nervous system	3.63e-25	53
regional part of brain	3.63e-25	53
ectoderm-derived structure	3.49e-20	171
ectoderm	3.49e-20	171
presumptive ectoderm	3.49e-20	171
neurectoderm	1.06e-19	86
regional part of forebrain	1.81e-18	41
forebrain	1.81e-18	41
anterior neural tube	1.81e-18	41
future forebrain	1.81e-18	41
neural plate	1.67e-17	82
presumptive neural plate	1.67e-17	82
brain grey matter	2.19e-17	34
gray matter	2.19e-17	34
telencephalon	2.67e-17	34
cerebral hemisphere	2.47e-16	32
regional part of telencephalon	4.88e-16	32
ecto-epithelium	1.25e-13	104
cerebral cortex	6.33e-13	25
pallium	6.33e-13	25
pre-chordal neural plate	3.33e-12	61
neocortex	1.15e-11	20
regional part of cerebral cortex	2.12e-11	22
posterior neural tube	1.01e-09	15
chordal neural plate	1.01e-09	15
adult organism	1.62e-09	114
organ part	6.76e-09	218
structure with developmental contribution from neural crest	2.18e-08	132
segmental subdivision of hindbrain	4.74e-08	12
hindbrain	4.74e-08	12
presumptive hindbrain	4.74e-08	12
segmental subdivision of nervous system	3.66e-07	13
anatomical cluster	8.34e-07	373

Disease

Ontology term	p-value	n
cell type cancer	1.90e-18	143
cancer	8.51e-17	235
disease of cellular proliferation	9.52e-16	239
germ cell and embryonal cancer	1.91e-11	22
germ cell cancer	1.91e-11	22
carcinoma	1.44e-09	106
neuroectodermal tumor	3.86e-09	10
gastrointestinal system cancer	2.72e-07	14

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)
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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
HEY1#23462	6	4.04011104310571	0.000229896855580751	0.00253245413985846
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380432089733036
SIN3A#25942	6	5.40888472681514	3.99207083571449e-05	0.000743054510802327
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00573343796898183

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.