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{{Coexpression_clusters
{
|full_id=C177_melanoma_Melanocyte_mesenchymal_retina_Mallassezderived_Gingival_squamous
|gostat_on_coexpression_clusters

Latest revision as of 10:49, 17 September 2013


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)
MA0003.17.44798e-12
MA0004.10.566052
MA0006.10.0350811
MA0007.10.0017566
MA0009.11.13589
MA0014.14.83151e-06
MA0017.10.210596
MA0019.10.16983
MA0024.10.061653
MA0025.10.170546
MA0027.11.4555
MA0028.10.00129978
MA0029.10.241246
MA0030.10.49665
MA0031.10.68278
MA0038.10.445814
MA0040.10.528809
MA0041.10.0185454
MA0042.10.102271
MA0043.10.102818
MA0046.10.0978884
MA0048.10.000141107
MA0050.10.103155
MA0051.10.249916
MA0052.13.81957
MA0055.10.00211192
MA0056.10
MA0057.10.00431148
MA0058.11.60942
MA0059.10.407669
MA0060.10.0147333
MA0061.10.000841846
MA0063.10
MA0066.10.0086217
MA0067.10.785233
MA0068.14.49145
MA0069.10.656129
MA0070.10.305732
MA0071.10.353067
MA0072.10.0895901
MA0073.10.000395383
MA0074.10.248686
MA0076.10.00457822
MA0077.10.291944
MA0078.10.229816
MA0081.10.0137996
MA0083.10.344888
MA0084.10.429854
MA0087.10.297857
MA0088.10.0924224
MA0089.10
MA0090.10.523863
MA0091.10.118986
MA0092.10.285349
MA0093.10.657538
MA0095.10
MA0098.10
MA0100.10.137059
MA0101.10.0801412
MA0103.10.0299854
MA0105.10.00466001
MA0106.10.0130334
MA0107.10.0845823
MA0108.20.379063
MA0109.10
MA0111.12.02034
MA0113.10.60135
MA0114.10.130285
MA0115.10.236407
MA0116.10.148746
MA0117.10.120117
MA0119.11.1743
MA0122.10.414695
MA0124.10.603604
MA0125.10.939192
MA0130.10
MA0131.10.024232
MA0132.10
MA0133.10
MA0135.10.75036
MA0136.10.463761
MA0139.10.010042
MA0140.10.347066
MA0141.11.0164
MA0142.11.355
MA0143.10.601856
MA0144.10.346269
MA0145.10.00349806
MA0146.11.34675e-07
MA0147.10.0524811
MA0148.10.919498
MA0149.10.00473599
MA0062.20.00211653
MA0035.21.81905
MA0039.21.21259e-07
MA0138.20.0928309
MA0002.20.761905
MA0137.20.41265
MA0104.20.0144344
MA0047.20.793015
MA0112.22.53958e-05
MA0065.20.0136198
MA0150.10.936581
MA0151.10
MA0152.10.361977
MA0153.10.151302
MA0154.10.000829132
MA0155.10.000727938
MA0156.10.285526
MA0157.10.122453
MA0158.10
MA0159.10.478699
MA0160.10.71837
MA0161.10
MA0162.18.81332e-07
MA0163.10.000305072
MA0164.10.637386
MA0080.20.341511
MA0018.20.0132062
MA0099.20.573623
MA0079.25.0145e-15
MA0102.20.459987
MA0258.10.00131953
MA0259.10.0609889
MA0442.10



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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