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Coexpression cluster:C177

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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

p.valueFDRnGenesnPathwayName
9.34407833048571e-050.02957400791598733121Lysosome (KEGG):04142
5.82213656356506e-050.02957400791598734295IL-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

GO IDGO nameFDR corrected p-value
GO:0009072aromatic amino acid family metabolic process0.0244980923056979
GO:0051066dihydrobiopterin metabolic process0.0244980923056979
GO:0042720mitochondrial inner membrane peptidase complex0.0244980923056979
GO:0004244mitochondrial inner membrane peptidase activity0.0244980923056979
GO:0004168dolichol kinase activity0.0244980923056979
GO:00041556,7-dihydropteridine reductase activity0.0244980923056979
GO:0005604basement membrane0.0244980923056979
GO:0015031protein transport0.0244980923056979
GO:0044444cytoplasmic part0.0244980923056979
GO:0046907intracellular transport0.0244980923056979
GO:0045184establishment of protein localization0.0244980923056979
GO:0006627mitochondrial protein processing0.0244980923056979
GO:0005737cytoplasm0.0244980923056979
GO:0008104protein localization0.0244980923056979
GO:0033036macromolecule localization0.0276871341969204
GO:0004167dopachrome isomerase activity0.0285100576328194
GO:0051649establishment of cellular localization0.0323570694221632
GO:0044420extracellular matrix part0.0323570694221632
GO:0051641cellular localization0.0323570694221632
GO:0006886intracellular protein transport0.0329806791542966
GO:0008333endosome to lysosome transport0.0337658358600434
GO:0006729tetrahydrobiopterin biosynthetic process0.0337658358600434
GO:0042438melanin biosynthetic process0.0337658358600434
GO:0033162melanosome membrane0.0337658358600434
GO:0006583melanin biosynthetic process from tyrosine0.0337658358600434
GO:0045009chitosome0.0337658358600434
GO:0030814regulation of cAMP metabolic process0.0337658358600434
GO:0016192vesicle-mediated transport0.034302368557875
GO:0046146tetrahydrobiopterin metabolic process0.034302368557875
GO:0030799regulation of cyclic nucleotide metabolic process0.034302368557875
GO:0006582melanin metabolic process0.034302368557875
GO:0006725aromatic compound metabolic process0.0353543814896279
GO:0005768endosome0.0364966712371678
GO:0043231intracellular membrane-bound organelle0.0364966712371678
GO:0043227membrane-bound organelle0.0364966712371678
GO:0051018protein kinase A binding0.0379597442071673
GO:0005095GTPase inhibitor activity0.0399482200961987
GO:0006140regulation of nucleotide metabolic process0.0399482200961987
GO:0006605protein targeting0.0407812542156949
GO:0031090organelle membrane0.0423437545104869
GO:0006558L-phenylalanine metabolic process0.0423437545104869
GO:0004065arylsulfatase activity0.0423437545104869
GO:0006559L-phenylalanine catabolic process0.0423437545104869
GO:0009003signal peptidase activity0.0448192957972126
GO:0007041lysosomal transport0.0471832292337848
GO:0006570tyrosine metabolic process0.0477529839959068
GO:0043408regulation of MAPKKK cascade0.0477529839959068
GO:0043229intracellular organelle0.0477529839959068
GO:0043226organelle0.0477529839959068



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>

Cell Type
Ontology termp-valuen
dark melanocyte3.99e-501
melanocyte8.54e-2110
melanoblast8.54e-2110
pigment cell3.41e-1514
neurecto-epithelial cell5.70e-1120
columnar/cuboidal epithelial cell2.14e-0827
ecto-epithelial cell7.16e-0734
glandular epithelial cell7.91e-079
Uber Anatomy
Ontology termp-valuen
retina1.57e-096
photoreceptor array1.57e-096
posterior segment of eyeball1.57e-096
Disease
Ontology termp-valuen
melanoma4.32e-262


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#promotersEnrichmentp-valueq-value
FOXA2#3170133.30098998747060.0001544128683098720.0019681139313418
RXRA#6256112.276502974540890.008966494544981560.0340008613674871



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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