Coexpression cluster:C171

Full id: C171_merkel_neuroblastoma_pineal_retinoblastoma_carcinoid_small_eye

Phase1 CAGE Peaks

Hg19::chr10:50604121..50604142,-	p1@DRGX
Hg19::chr10:50606625..50606638,-	p@chr10:50606625..50606638 -
Hg19::chr11:128634589..128634606,+	p14@FLI1
Hg19::chr11:20182017..20182023,-	p1@DBX1
Hg19::chr11:64834320..64834330,-	p@chr11:64834320..64834330 -
Hg19::chr11:66495843..66495860,-	p@chr11:66495843..66495860 -
Hg19::chr11:79659013..79659021,-	p@chr11:79659013..79659021 -
Hg19::chr11:79659052..79659060,-	p@chr11:79659052..79659060 -
Hg19::chr11:88953463..88953464,-	p@chr11:88953463..88953464 -
Hg19::chr12:16941106..16941119,-	p@chr12:16941106..16941119 -
Hg19::chr12:58212511..58212522,-	p1@AVIL
Hg19::chr12:58212533..58212539,-	p2@AVIL
Hg19::chr13:112161853..112161860,-	p@chr13:112161853..112161860 -
Hg19::chr15:46610847..46610851,+	p@chr15:46610847..46610851 +
Hg19::chr15:46610897..46610904,+	p@chr15:46610897..46610904 +
Hg19::chr16:2518541..2518589,-	p1@LOC729652
Hg19::chr16:3063137..3063169,+	p3@CLDN9
Hg19::chr16:81253986..81254016,-	p10@PKD1L2
Hg19::chr17:56033198..56033217,-	p@chr17:56033198..56033217 -
Hg19::chr17:78070711..78070726,+	p@chr17:78070711..78070726 +
Hg19::chr17:78083663..78083704,+	p@chr17:78083663..78083704 +
Hg19::chr17:78083724..78083737,+	p@chr17:78083724..78083737 +
Hg19::chr17:78083748..78083757,+	p@chr17:78083748..78083757 +
Hg19::chr18:13165683..13165695,-	p@chr18:13165683..13165695 -
Hg19::chr19:13648652..13648664,+	p@chr19:13648652..13648664 +
Hg19::chr19:893600..893603,+	p@chr19:893600..893603 +
Hg19::chr1:10926182..10926191,-	p@chr1:10926182..10926191 -
Hg19::chr1:155048171..155048179,+	p@chr1:155048171..155048179 +
Hg19::chr1:159915336..159915350,-	p@chr1:159915336..159915350 -
Hg19::chr1:160336851..160336868,+	p1@NHLH1
Hg19::chr1:160336929..160336938,+	p2@NHLH1
Hg19::chr1:203491082..203491114,-	p@chr1:203491082..203491114 -
Hg19::chr1:20609411..20609416,+	p@chr1:20609411..20609416 +
Hg19::chr1:215892699..215892705,-	p@chr1:215892699..215892705 -
Hg19::chr1:216286476..216286479,-	p@chr1:216286476..216286479 -
Hg19::chr1:216293559..216293561,-	p@chr1:216293559..216293561 -
Hg19::chr1:216596783..216596796,-	p1@USH2A
Hg19::chr1:33338030..33338037,-	p9@FNDC5
Hg19::chr1:3575730..3575736,-	p@chr1:3575730..3575736 -
Hg19::chr1:3585331..3585373,-	p1@ENST00000443034
Hg19::chr1:3585377..3585386,-	p4@ENST00000443034
Hg19::chr1:3585412..3585417,-	p5@ENST00000443034
Hg19::chr1:3585436..3585446,-	p3@ENST00000443034
Hg19::chr1:3585501..3585512,-	p2@ENST00000443034
Hg19::chr1:3585598..3585610,+	p@chr1:3585598..3585610 +
Hg19::chr1:3607219..3607226,+	p16@TP73
Hg19::chr1:3607228..3607250,+	p8@TP73
Hg19::chr1:3607263..3607274,+	p12@TP73
Hg19::chr1:3607281..3607291,+	p13@TP73
Hg19::chr1:3607307..3607317,+	p15@TP73
Hg19::chr1:3608060..3608071,-	p@chr1:3608060..3608071 -
Hg19::chr1:3844945..3844991,+	p@chr1:3844945..3844991 +
Hg19::chr20:62791809..62791857,+	p@chr20:62791809..62791857 +
Hg19::chr21:33976741..33976754,-	p16@C21orf59
Hg19::chr21:33976794..33976805,-	p14@C21orf59
Hg19::chr21:33976809..33976828,-	p9@C21orf59
Hg19::chr22:27043104..27043111,+	p27@MIAT
Hg19::chr22:35568509..35568524,-	p@chr22:35568509..35568524 -
Hg19::chr22:35568566..35568568,-	p@chr22:35568566..35568568 -
Hg19::chr22:35921483..35921490,-	p@chr22:35921483..35921490 -
Hg19::chr22:50942880..50942889,-	p@chr22:50942880..50942889 -
Hg19::chr2:133025802..133025846,-	p@chr2:133025802..133025846 -
Hg19::chr2:226264508..226264517,+	p3@ENST00000431435
Hg19::chr2:3152671..3152679,-	p@chr2:3152671..3152679 -
Hg19::chr2:51255204..51255216,-	p36@NRXN1
Hg19::chr2:51255218..51255229,-	p55@NRXN1
Hg19::chr2:51255231..51255244,-	p38@NRXN1
Hg19::chr2:51255365..51255374,+	p@chr2:51255365..51255374 +
Hg19::chr3:134151281..134151311,+	p@chr3:134151281..134151311 +
Hg19::chr3:140770183..140770206,+	p1@SPSB4
Hg19::chr3:140770345..140770394,+	p5@SPSB4
Hg19::chr3:140784752..140784757,+	p10@SPSB4
Hg19::chr3:66452082..66452087,-	p@chr3:66452082..66452087 -
Hg19::chr3:7994758..7994778,-	p@chr3:7994758..7994778 -
Hg19::chr4:100574051..100574060,-	p@chr4:100574051..100574060 -
Hg19::chr4:82619895..82619898,-	p@chr4:82619895..82619898 -
Hg19::chr5:14742023..14742037,-	p@chr5:14742023..14742037 -
Hg19::chr7:1272522..1272537,+	p2@UNCX
Hg19::chr7:155363439..155363470,-	p@chr7:155363439..155363470 -
Hg19::chr8:64349920..64349932,+	p@chr8:64349920..64349932 +
Hg19::chr8:80992779..80992802,-	p12@TPD52
Hg19::chr9:11199497..11199506,-	p@chr9:11199497..11199506 -
Hg19::chr9:133354532..133354539,+	p@chr9:133354532..133354539 +
Hg19::chr9:133355042..133355052,+	p10@ASS1
Hg19::chr9:133355076..133355092,+	p9@ASS1
Hg19::chr9:135433343..135433346,-	p@chr9:135433343..135433346 -
Hg19::chr9:136450600..136450606,+	p@chr9:136450600..136450606 +
Hg19::chr9:139085557..139085584,-	p1@RBSG2
Hg19::chr9:139091058..139091074,-	p@chr9:139091058..139091074 -
Hg19::chr9:139091385..139091433,-	p@chr9:139091385..139091433 -
Hg19::chr9:139094988..139095012,-	p1@LHX3
Hg19::chr9:139095013..139095024,-	p3@LHX3
Hg19::chr9:139095030..139095040,-	p4@LHX3
Hg19::chr9:139096259..139096268,-	p@chr9:139096259..139096268 -
Hg19::chr9:139096968..139096979,-	p2@LHX3
Hg19::chr9:33719626..33719633,-	p@chr9:33719626..33719633 -
Hg19::chr9:33719660..33719671,-	p@chr9:33719660..33719671 -
Hg19::chr9:38414152..38414168,-	p@chr9:38414152..38414168 -
Hg19::chr9:38414288..38414301,-	p@chr9:38414288..38414301 -
Hg19::chr9:38414310..38414331,-	p@chr9:38414310..38414331 -
Hg19::chr9:38414334..38414354,-	p@chr9:38414334..38414354 -

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:0007275	multicellular organismal development	0.000641210868674468
GO:0032502	developmental process	0.000641210868674468
GO:0048856	anatomical structure development	0.00144825555041831
GO:0043565	sequence-specific DNA binding	0.00197243719679013
GO:0003700	transcription factor activity	0.00197243719679013
GO:0048731	system development	0.00241078521397418
GO:0044424	intracellular part	0.00438791712875587
GO:0032501	multicellular organismal process	0.00438791712875587
GO:0019222	regulation of metabolic process	0.00699071498393437
GO:0050794	regulation of cellular process	0.00955040933301972
GO:0006355	regulation of transcription, DNA-dependent	0.0103851039816391
GO:0006351	transcription, DNA-dependent	0.0103851039816391
GO:0032774	RNA biosynthetic process	0.0103851039816391
GO:0003677	DNA binding	0.010758642121758
GO:0050789	regulation of biological process	0.0112451306537117
GO:0045449	regulation of transcription	0.0118718949045196
GO:0065008	regulation of biological quality	0.0118718949045196
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0118718949045196
GO:0006350	transcription	0.0128681907351291
GO:0010468	regulation of gene expression	0.0128681907351291
GO:0005622	intracellular	0.0128681907351291
GO:0009653	anatomical structure morphogenesis	0.0131530478983111
GO:0031323	regulation of cellular metabolic process	0.0131530478983111
GO:0065007	biological regulation	0.0141190093803605
GO:0048513	organ development	0.0161555509443677
GO:0016070	RNA metabolic process	0.0161555509443677
GO:0048496	maintenance of organ identity	0.0172228248639993
GO:0002347	response to tumor cell	0.0249005894688049
GO:0005634	nucleus	0.0284863001369077
GO:0043603	amide metabolic process	0.0290378655176246
GO:0019627	urea metabolic process	0.0290378655176246
GO:0000050	urea cycle	0.0290378655176246
GO:0004055	argininosuccinate synthase activity	0.0316706804307545
GO:0044464	cell part	0.0447072753794081
GO:0045494	photoreceptor cell maintenance	0.0497023599078022

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
Merkel cell	3.29e-195	2
keratinocyte	3.49e-79	5
stratified squamous epithelial cell	2.83e-66	6
keratin accumulating cell	2.83e-66	6
stratified epithelial cell	2.83e-66	6
keratinizing barrier epithelial cell	2.83e-66	6
epithelial fate stem cell	2.83e-66	6
stratified epithelial stem cell	2.83e-66	6
surface ectodermal cell	2.83e-66	6
epidermal cell	9.75e-45	9
general ecto-epithelial cell	2.55e-29	14
neuron associated cell	5.37e-22	17
neuron associated cell (sensu Vertebrata)	5.37e-22	17
single fate stem cell	5.71e-21	20
neural cell	6.71e-16	25
ecto-epithelial cell	6.62e-13	34
migratory neural crest cell	1.77e-10	41
neurectodermal cell	9.44e-08	59
squamous epithelial cell	1.52e-07	63

Uber Anatomy

Ontology term	p-value	n
skin epidermis	1.82e-27	15
outer epithelium	1.82e-27	15
enveloping layer of ectoderm	1.82e-27	15
skin of body	6.32e-11	41
integument	7.07e-10	46
integumental system	7.07e-10	46

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
SUZ12#23512	9	4.46576265544125	0.000199548401979449	0.00239575072471912

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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