Coexpression cluster:C740

Full id: C740_gastrointestinal_smallcell_small_nonsmall_neuroblastoma_temporal_somatostatinoma

Phase1 CAGE Peaks

Hg19::chr11:60466937..60466947,+	p6@MS4A8B
Hg19::chr12:103351444..103351461,+	p1@ASCL1
Hg19::chr12:103351694..103351704,+	p6@ASCL1
Hg19::chr12:103352731..103352740,+	p@chr12:103352731..103352740 +
Hg19::chr12:103353138..103353168,+	p@chr12:103353138..103353168 +
Hg19::chr12:103353295..103353316,-	p@chr12:103353295..103353316 -
Hg19::chr12:103353566..103353596,+	p@chr12:103353566..103353596 +
Hg19::chr16:67219381..67219395,-	p@chr16:67219381..67219395 -
Hg19::chr17:17421463..17421482,-	p5@PEMT
Hg19::chr19:13743837..13743844,-	p@chr19:13743837..13743844 -
Hg19::chr1:246383189..246383211,-	p@chr1:246383189..246383211 -

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0060163	subpallium neuron fate commitment	0.00152646717464803
GO:0014017	neuroblast fate commitment	0.00152646717464803
GO:0014016	neuroblast differentiation	0.00152646717464803
GO:0007400	neuroblast fate determination	0.00152646717464803
GO:0060165	regulation of timing of subpallium neuron differentiation	0.00152646717464803
GO:0060164	regulation of timing of neuron differentiation	0.00152646717464803
GO:0004608	phosphatidylethanolamine N-methyltransferase activity	0.00152646717464803
GO:0021544	subpallium development	0.00400674043006203
GO:0048505	regulation of timing of cell differentiation	0.00427373064729577
GO:0040034	regulation of development, heterochronic	0.00427373064729577
GO:0006656	phosphatidylcholine biosynthetic process	0.00485636913446346
GO:0046470	phosphatidylcholine metabolic process	0.00623197345720764
GO:0021537	telencephalon development	0.0090387212307888
GO:0048663	neuron fate commitment	0.0106811816718229
GO:0008283	cell proliferation	0.0113477532025367
GO:0007405	neuroblast proliferation	0.0113477532025367
GO:0045664	regulation of neuron differentiation	0.0162956577304724
GO:0010001	glial cell differentiation	0.0162956577304724
GO:0001709	cell fate determination	0.0162956577304724
GO:0042063	gliogenesis	0.0182987399358394
GO:0001764	neuron migration	0.0182987399358394
GO:0030900	forebrain development	0.0213397299517958
GO:0046474	glycerophospholipid biosynthetic process	0.0213397299517958
GO:0008170	N-methyltransferase activity	0.0213397299517958
GO:0007219	Notch signaling pathway	0.0213397299517958
GO:0045165	cell fate commitment	0.0291189221451797
GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	0.0339494755587485
GO:0008654	phospholipid biosynthetic process	0.0350147803328724
GO:0006650	glycerophospholipid metabolic process	0.0371047763843612
GO:0046467	membrane lipid biosynthetic process	0.0401153013644764
GO:0007389	pattern specification process	0.0425865120099492
GO:0007420	brain development	0.0462258483643068
GO:0045595	regulation of cell differentiation	0.0464306336375757
GO:0048666	neuron development	0.0481803368997648

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>

---

Cell Type

Ontology term	p-value	n
circulating cell	2.77e-07	6

Uber Anatomy

Ontology term	p-value	n
neural tube	1.07e-30	56
neural rod	1.07e-30	56
future spinal cord	1.07e-30	56
neural keel	1.07e-30	56
central nervous system	1.19e-23	81
regional part of nervous system	1.51e-23	53
regional part of brain	1.51e-23	53
nervous system	6.35e-23	89
neural plate	1.77e-21	82
presumptive neural plate	1.77e-21	82
neurectoderm	3.06e-20	86
brain	3.46e-19	68
future brain	3.46e-19	68
regional part of forebrain	4.04e-19	41
forebrain	4.04e-19	41
anterior neural tube	4.04e-19	41
future forebrain	4.04e-19	41
ecto-epithelium	1.49e-17	104
telencephalon	1.21e-14	34
spinal cord	3.45e-14	3
dorsal region element	3.45e-14	3
dorsum	3.45e-14	3
pre-chordal neural plate	1.11e-13	61
posterior neural tube	3.04e-13	15
chordal neural plate	3.04e-13	15
regional part of cerebral cortex	3.10e-13	22
regional part of telencephalon	3.84e-13	32
cerebral hemisphere	3.84e-13	32
adult organism	1.26e-12	114
brain grey matter	2.88e-12	34
gray matter	2.88e-12	34
neocortex	1.49e-11	20
cerebral cortex	1.58e-11	25
pallium	1.58e-11	25
ectoderm-derived structure	1.64e-11	171
ectoderm	1.64e-11	171
presumptive ectoderm	1.64e-11	171
structure with developmental contribution from neural crest	2.13e-11	132
organ system subdivision	5.90e-11	223
pituitary gland	4.34e-10	2
tube	5.52e-08	192
brainstem	7.58e-07	6
gyrus	7.73e-07	6

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

---

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

---

(#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	11.4030909707869	0.0127037060978319	0.0458357756218981
SPI1#6688	5	3.72923795841942	0.00657139769228244	0.0280848796326998
SUZ12#23512	4	18.2239203312956	4.66826240794143e-05	0.000816664418128969

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

---

This analysis result is provided for C0 - C305 clusters.