Coexpression cluster:C177

Full id: C177_melanoma_Melanocyte_mesenchymal_retina_Mallassezderived_Gingival_squamous

Phase1 CAGE Peaks

Hg19::chr10:14116696..14116703,+	p4@ENST00000451617
Hg19::chr10:77360969..77360998,+	p@chr10:77360969..77360998 +
Hg19::chr10:77360999..77361028,+	p@chr10:77360999..77361028 +
Hg19::chr10:93335031..93335040,-	p2@BC044257
Hg19::chr11:20791058..20791067,+	p10@NELL1
Hg19::chr11:20792354..20792385,+	p3@NELL1
Hg19::chr12:100985946..100985951,+	p@chr12:100985946..100985951 +
Hg19::chr12:15077186..15077193,-	p@chr12:15077186..15077193 -
Hg19::chr12:56120865..56120875,-	p39@CD63
Hg19::chr13:95121086..95121093,-	p11@DCT
Hg19::chr13:95131368..95131378,-	p2@CU688450
Hg19::chr13:95131390..95131397,-	p3@CU688450
Hg19::chr13:95131432..95131447,-	p4@DCT
Hg19::chr13:95131475..95131494,-	p7@DCT
Hg19::chr13:95131529..95131538,+	p@chr13:95131529..95131538 +
Hg19::chr13:95131539..95131548,+	p@chr13:95131539..95131548 +
Hg19::chr13:95131822..95131842,-	p2@DCT
Hg19::chr13:95131926..95131944,-	p1@DCT
Hg19::chr13:95132078..95132083,-	p8@DCT
Hg19::chr13:95165454..95165463,-	p@chr13:95165454..95165463 -
Hg19::chr13:95168223..95168271,-	p@chr13:95168223..95168271 -
Hg19::chr14:32963209..32963217,+	p21@AKAP6
Hg19::chr14:32963254..32963261,+	p19@AKAP6
Hg19::chr14:36536424..36536433,-	p1@ENST00000546376
Hg19::chr14:36536439..36536442,-	p3@ENST00000546376
Hg19::chr15:80603266..80603271,-	p@chr15:80603266..80603271 -
Hg19::chr15:93267558..93267561,-	p22@FAM174B
Hg19::chr17:65214809..65214830,-	p1@AB463064
Hg19::chr17:66396581..66396600,+	p8@ARSG
Hg19::chr17:75314660..75314675,+	p@chr17:75314660..75314675 +
Hg19::chr17:75314684..75314694,+	p@chr17:75314684..75314694 +
Hg19::chr17:76870102..76870114,-	p35@TIMP2
Hg19::chr18:14946224..14946236,+	p1@FLJ44255
Hg19::chr19:19637851..19637862,+	p@chr19:19637851..19637862 +
Hg19::chr19:19637865..19637872,+	p@chr19:19637865..19637872 +
Hg19::chr19:19638023..19638028,+	p@chr19:19638023..19638028 +
Hg19::chr19:19639710..19639727,+	p2@YJEFN3
Hg19::chr19:35890402..35890413,+	p@chr19:35890402..35890413 +
Hg19::chr19:35890435..35890446,+	p@chr19:35890435..35890446 +
Hg19::chr1:144866743..144866748,-	p71@PDE4DIP
Hg19::chr1:144866760..144866765,-	p78@PDE4DIP
Hg19::chr1:144866830..144866835,-	p74@PDE4DIP
Hg19::chr1:144866839..144866843,-	p77@PDE4DIP
Hg19::chr1:144866845..144866850,-	p72@PDE4DIP
Hg19::chr1:144866854..144866864,-	p62@PDE4DIP
Hg19::chr1:144866866..144866877,-	p61@PDE4DIP
Hg19::chr1:207070775..207070797,+	p1@IL24
Hg19::chr1:207070909..207070932,+	p2@IL24
Hg19::chr1:207076414..207076427,+	p@chr1:207076414..207076427 +
Hg19::chr1:207076932..207076936,+	p@chr1:207076932..207076936 +
Hg19::chr1:236046908..236046924,-	p10@LYST
Hg19::chr1:236046960..236047018,-	p3@LYST
Hg19::chr1:236047109..236047114,-	p23@LYST
Hg19::chr1:240502414..240502420,+	p@chr1:240502414..240502420 +
Hg19::chr1:240569692..240569715,+	p@chr1:240569692..240569715 +
Hg19::chr1:240569735..240569744,+	p@chr1:240569735..240569744 +
Hg19::chr1:51763637..51763651,-	p6@TTC39A
Hg19::chr1:51763661..51763672,-	p11@TTC39A
Hg19::chr1:84885042..84885045,-	p@chr1:84885042..84885045 -
Hg19::chr20:50179584..50179611,-	p6@NFATC2
Hg19::chr2:135170141..135170155,+	p@chr2:135170141..135170155 +
Hg19::chr2:135170164..135170181,+	p@chr2:135170164..135170181 +
Hg19::chr2:135170187..135170199,+	p@chr2:135170187..135170199 +
Hg19::chr2:135170207..135170218,+	p@chr2:135170207..135170218 +
Hg19::chr2:135170267..135170276,+	p@chr2:135170267..135170276 +
Hg19::chr2:135170340..135170356,+	p@chr2:135170340..135170356 +
Hg19::chr2:135170403..135170416,+	p@chr2:135170403..135170416 +
Hg19::chr2:166702828..166702850,-	p4@ENST00000428888
Hg19::chr2:234875290..234875297,+	p13@TRPM8
Hg19::chr2:234875305..234875314,+	p12@TRPM8
Hg19::chr2:234882762..234882776,+	p@chr2:234882762..234882776 +
Hg19::chr2:37501692..37501712,-	p@chr2:37501692..37501712 -
Hg19::chr2:48274017..48274020,+	p@chr2:48274017..48274020 +
Hg19::chr2:85987839..85987846,+	p20@ATOH8
Hg19::chr3:15727629..15727644,-	p@chr3:15727629..15727644 -
Hg19::chr4:17494021..17494040,-	p10@QDPR
Hg19::chr4:31101233..31101238,-	p@chr4:31101233..31101238 -
Hg19::chr5:38148587..38148600,+	p1@ENST00000508853
Hg19::chr5:75970339..75970366,+	p19@IQGAP2
Hg19::chr6:134871317..134871322,+	p@chr6:134871317..134871322 +
Hg19::chr6:165597253..165597261,-	p@chr6:165597253..165597261 -
Hg19::chr6:165597276..165597281,-	p@chr6:165597276..165597281 -
Hg19::chr6:96188999..96189001,-	p@chr6:96188999..96189001 -
Hg19::chr7:104420654..104420668,+	p@chr7:104420654..104420668 +
Hg19::chr7:111032997..111033020,-	p6@IMMP2L
Hg19::chr7:29898603..29898606,+	p@chr7:29898603..29898606 +
Hg19::chr7:46799446..46799457,-	p1@ENST00000487094
Hg19::chr7:80116896..80116907,+	p@chr7:80116896..80116907 +
Hg19::chr8:105044082..105044088,-	p@chr8:105044082..105044088 -
Hg19::chr8:42013399..42013411,+	p5@AP3M2
Hg19::chr9:105414888..105414895,-	p@chr9:105414888..105414895 -
Hg19::chr9:105414902..105414913,-	p@chr9:105414902..105414913 -
Hg19::chr9:12554659..12554671,-	p@chr9:12554659..12554671 -
Hg19::chr9:14869205..14869217,-	p17@FREM1
Hg19::chr9:14869264..14869271,-	p27@FREM1
Hg19::chr9:2732098..2732101,-	p@chr9:2732098..2732101 -
Hg19::chr9:71922022..71922051,-	p@chr9:71922022..71922051 -

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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p.value	FDR	nGenes	nPathway	Name
9.34407833048571e-05	0.0295740079159873	3	121	Lysosome (KEGG):04142
5.82213656356506e-05	0.0295740079159873	4	295	IL-2 down reg. targets (Netpath):NetPath_14

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:0009072	aromatic amino acid family metabolic process	0.0244980923056979
GO:0051066	dihydrobiopterin metabolic process	0.0244980923056979
GO:0042720	mitochondrial inner membrane peptidase complex	0.0244980923056979
GO:0004244	mitochondrial inner membrane peptidase activity	0.0244980923056979
GO:0004168	dolichol kinase activity	0.0244980923056979
GO:0004155	6,7-dihydropteridine reductase activity	0.0244980923056979
GO:0005604	basement membrane	0.0244980923056979
GO:0015031	protein transport	0.0244980923056979
GO:0044444	cytoplasmic part	0.0244980923056979
GO:0046907	intracellular transport	0.0244980923056979
GO:0045184	establishment of protein localization	0.0244980923056979
GO:0006627	mitochondrial protein processing	0.0244980923056979
GO:0005737	cytoplasm	0.0244980923056979
GO:0008104	protein localization	0.0244980923056979
GO:0033036	macromolecule localization	0.0276871341969204
GO:0004167	dopachrome isomerase activity	0.0285100576328194
GO:0051649	establishment of cellular localization	0.0323570694221632
GO:0044420	extracellular matrix part	0.0323570694221632
GO:0051641	cellular localization	0.0323570694221632
GO:0006886	intracellular protein transport	0.0329806791542966
GO:0008333	endosome to lysosome transport	0.0337658358600434
GO:0006729	tetrahydrobiopterin biosynthetic process	0.0337658358600434
GO:0042438	melanin biosynthetic process	0.0337658358600434
GO:0033162	melanosome membrane	0.0337658358600434
GO:0006583	melanin biosynthetic process from tyrosine	0.0337658358600434
GO:0045009	chitosome	0.0337658358600434
GO:0030814	regulation of cAMP metabolic process	0.0337658358600434
GO:0016192	vesicle-mediated transport	0.034302368557875
GO:0046146	tetrahydrobiopterin metabolic process	0.034302368557875
GO:0030799	regulation of cyclic nucleotide metabolic process	0.034302368557875
GO:0006582	melanin metabolic process	0.034302368557875
GO:0006725	aromatic compound metabolic process	0.0353543814896279
GO:0005768	endosome	0.0364966712371678
GO:0043231	intracellular membrane-bound organelle	0.0364966712371678
GO:0043227	membrane-bound organelle	0.0364966712371678
GO:0051018	protein kinase A binding	0.0379597442071673
GO:0005095	GTPase inhibitor activity	0.0399482200961987
GO:0006140	regulation of nucleotide metabolic process	0.0399482200961987
GO:0006605	protein targeting	0.0407812542156949
GO:0031090	organelle membrane	0.0423437545104869
GO:0006558	L-phenylalanine metabolic process	0.0423437545104869
GO:0004065	arylsulfatase activity	0.0423437545104869
GO:0006559	L-phenylalanine catabolic process	0.0423437545104869
GO:0009003	signal peptidase activity	0.0448192957972126
GO:0007041	lysosomal transport	0.0471832292337848
GO:0006570	tyrosine metabolic process	0.0477529839959068
GO:0043408	regulation of MAPKKK cascade	0.0477529839959068
GO:0043229	intracellular organelle	0.0477529839959068
GO:0043226	organelle	0.0477529839959068

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
dark melanocyte	3.99e-50	1
melanocyte	8.54e-21	10
melanoblast	8.54e-21	10
pigment cell	3.41e-15	14
neurecto-epithelial cell	5.70e-11	20
columnar/cuboidal epithelial cell	2.14e-08	27
ecto-epithelial cell	7.16e-07	34
glandular epithelial cell	7.91e-07	9

Uber Anatomy

Ontology term	p-value	n
retina	1.57e-09	6
photoreceptor array	1.57e-09	6
posterior segment of eyeball	1.57e-09	6

Disease

Ontology term	p-value	n
melanoma	4.32e-26	2

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
FOXA2#3170	13	3.3009899874706	0.000154412868309872	0.0019681139313418
RXRA#6256	11	2.27650297454089	0.00896649454498156	0.0340008613674871

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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