Coexpression cluster:C939

Full id: C939_neuroblastoma_argyrophil_small_cerebellum_retinoblastoma_pineal_medulloblastoma

Phase1 CAGE Peaks

Hg19::chr2:182543057..182543068,-	p1@GQ904713
Hg19::chr2:182543197..182543218,-	p4@NEUROD1
Hg19::chr2:182543249..182543261,-	p5@NEUROD1
Hg19::chr2:182543547..182543559,-	p9@NEUROD1
Hg19::chr2:182545234..182545252,-	p1@NEUROD1
Hg19::chr2:182545296..182545307,-	p3@NEUROD1
Hg19::chr2:182545330..182545341,-	p2@CERKL
Hg19::chr2:182545363..182545372,-	p3@CERKL
Hg19::chr6:66194027..66194031,-	p@chr6:66194027..66194031 -

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:0030902	hindbrain development	0.0428039440196433
GO:0004143	diacylglycerol kinase activity	0.0428039440196433
GO:0043010	camera-type eye development	0.0428039440196433
GO:0007205	protein kinase C activation	0.0428039440196433
GO:0001654	eye development	0.0428039440196433
GO:0009952	anterior/posterior pattern formation	0.0428039440196433
GO:0032147	activation of protein kinase activity	0.0428039440196433
GO:0045165	cell fate commitment	0.0428039440196433
GO:0007423	sensory organ development	0.0428039440196433
GO:0003002	regionalization	0.0428039440196433
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.0428039440196433
GO:0007389	pattern specification process	0.0436576993985432
GO:0048015	phosphoinositide-mediated signaling	0.0436576993985432
GO:0007420	brain development	0.0436576993985432
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0436576993985432
GO:0045860	positive regulation of protein kinase activity	0.0436576993985432
GO:0033674	positive regulation of kinase activity	0.0436576993985432
GO:0051347	positive regulation of transferase activity	0.0436576993985432
GO:0032501	multicellular organismal process	0.0496195203628137
GO:0007601	visual perception	0.0496195203628137
GO:0050953	sensory perception of light stimulus	0.0496195203628137
GO:0045893	positive regulation of transcription, DNA-dependent	0.0496195203628137
GO:0007417	central nervous system development	0.0496195203628137
GO:0045859	regulation of protein kinase activity	0.0496195203628137
GO:0043549	regulation of kinase activity	0.0496195203628137
GO:0051338	regulation of transferase activity	0.0496195203628137
GO:0043085	positive regulation of catalytic activity	0.0496195203628137
GO:0019932	second-messenger-mediated signaling	0.0496195203628137
GO:0003702	RNA polymerase II transcription factor activity	0.0496195203628137
GO:0045941	positive regulation of transcription	0.0496195203628137
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0497326468379995

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	4.73e-07	25

Uber Anatomy

Ontology term	p-value	n
central nervous system	1.08e-56	82
regional part of nervous system	6.12e-53	94
nervous system	6.12e-53	94
neural tube	1.22e-52	57
neural rod	1.22e-52	57
future spinal cord	1.22e-52	57
neural keel	1.22e-52	57
brain	8.28e-48	69
future brain	8.28e-48	69
regional part of brain	5.88e-46	59
neural plate	7.11e-41	86
presumptive neural plate	7.11e-41	86
regional part of forebrain	2.48e-40	41
forebrain	2.48e-40	41
future forebrain	2.48e-40	41
neurectoderm	3.95e-40	90
anterior neural tube	3.96e-39	42
regional part of cerebral cortex	2.01e-37	22
cerebral cortex	4.58e-35	25
pallium	4.58e-35	25
neocortex	4.03e-34	20
telencephalon	2.93e-33	34
gray matter	3.99e-33	34
brain grey matter	3.99e-33	34
regional part of telencephalon	8.34e-32	33
pre-chordal neural plate	3.62e-31	61
cerebral hemisphere	6.38e-31	32
adult organism	6.02e-30	115
ectoderm	3.80e-27	173
presumptive ectoderm	3.80e-27	173
ectoderm-derived structure	4.23e-27	169
anterior region of body	1.31e-25	129
craniocervical region	1.31e-25	129
head	2.44e-25	123
temporal lobe	2.61e-14	7
posterior neural tube	3.72e-14	15
chordal neural plate	3.72e-14	15
segmental subdivision of hindbrain	3.40e-13	12
hindbrain	3.40e-13	12
presumptive hindbrain	3.40e-13	12
segmental subdivision of nervous system	5.48e-12	13
regional part of metencephalon	9.60e-12	9
metencephalon	9.60e-12	9
future metencephalon	9.60e-12	9
gyrus	1.19e-10	6
limbic system	1.48e-09	5
occipital lobe	2.59e-09	5
parietal lobe	3.03e-09	5
tube	3.39e-09	194
diencephalon	2.19e-08	7
future diencephalon	2.19e-08	7
cerebellum	6.46e-08	6
rhombic lip	6.46e-08	6
organ part	7.28e-08	219
gland of diencephalon	9.03e-08	4
neuroendocrine gland	9.03e-08	4
brainstem	6.14e-07	8

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
ATF3#467	4	9.98363312267056	0.000412784327724188	0.00393203050010822
NRF1#4899	4	5.42679086564929	0.00404669891206852	0.0193681860445225
REST#5978	4	4.28890165161245	0.00945702594596283	0.0356705671122255
SUZ12#23512	2	11.1368402024584	0.0130543531390231	0.0463121569172334
TCF12#6938	4	4.72642884541619	0.00668035530260397	0.0284202870768119
USF2#7392	4	5.77430994891982	0.00322324100537492	0.016701332970845
ZNF263#10127	8	7.30830367734282	3.84008362723504e-07	1.8758395413695e-05

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.