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{{Coexpression_clusters
{
|full_id=C171_merkel_neuroblastoma_pineal_retinoblastoma_carcinoid_small_eye
 

Latest revision as of 10:48, 17 September 2013


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

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

GO IDGO nameFDR corrected p-value
GO:0007275multicellular organismal development0.000641210868674468
GO:0032502developmental process0.000641210868674468
GO:0048856anatomical structure development0.00144825555041831
GO:0043565sequence-specific DNA binding0.00197243719679013
GO:0003700transcription factor activity0.00197243719679013
GO:0048731system development0.00241078521397418
GO:0044424intracellular part0.00438791712875587
GO:0032501multicellular organismal process0.00438791712875587
GO:0019222regulation of metabolic process0.00699071498393437
GO:0050794regulation of cellular process0.00955040933301972
GO:0006355regulation of transcription, DNA-dependent0.0103851039816391
GO:0006351transcription, DNA-dependent0.0103851039816391
GO:0032774RNA biosynthetic process0.0103851039816391
GO:0003677DNA binding0.010758642121758
GO:0050789regulation of biological process0.0112451306537117
GO:0045449regulation of transcription0.0118718949045196
GO:0065008regulation of biological quality0.0118718949045196
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0118718949045196
GO:0006350transcription0.0128681907351291
GO:0010468regulation of gene expression0.0128681907351291
GO:0005622intracellular0.0128681907351291
GO:0009653anatomical structure morphogenesis0.0131530478983111
GO:0031323regulation of cellular metabolic process0.0131530478983111
GO:0065007biological regulation0.0141190093803605
GO:0048513organ development0.0161555509443677
GO:0016070RNA metabolic process0.0161555509443677
GO:0048496maintenance of organ identity0.0172228248639993
GO:0002347response to tumor cell0.0249005894688049
GO:0005634nucleus0.0284863001369077
GO:0043603amide metabolic process0.0290378655176246
GO:0019627urea metabolic process0.0290378655176246
GO:0000050urea cycle0.0290378655176246
GO:0004055argininosuccinate synthase activity0.0316706804307545
GO:0044464cell part0.0447072753794081
GO:0045494photoreceptor cell maintenance0.0497023599078022



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>

Uber Anatomy
Ontology termp-valuen
skin epidermis1.82e-2715
outer epithelium1.82e-2715
enveloping layer of ectoderm1.82e-2715
skin of body6.32e-1141
integument7.07e-1046
integumental system7.07e-1046


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)
MA0003.14.97449
MA0004.10.336206
MA0006.10.57222
MA0007.10.453501
MA0009.10.652847
MA0014.11.76752
MA0017.10.594403
MA0019.10.309057
MA0024.10.0563848
MA0025.10.161182
MA0027.11.43827
MA0028.10.014832
MA0029.10.225004
MA0030.10.467498
MA0031.10.358359
MA0038.10.232786
MA0040.10.230819
MA0041.10.120738
MA0042.10.678115
MA0043.10.0956642
MA0046.10.0909318
MA0048.13.19302
MA0050.10.0896006
MA0051.10.226209
MA0052.10.868458
MA0055.17.29625
MA0056.10
MA0057.10.210667
MA0058.10.0326375
MA0059.10.716129
MA0060.10.26304
MA0061.10.0403038
MA0063.10
MA0066.12.47396
MA0067.10.276424
MA0068.10.891605
MA0069.11.04297
MA0070.11.01017
MA0071.10.514109
MA0072.10.0829813
MA0073.19.47688
MA0074.10.89594
MA0076.10.00361062
MA0077.10.577062
MA0078.10.985937
MA0081.10.139178
MA0083.10.32547
MA0084.10.416137
MA0087.10.587317
MA0088.11.5697
MA0089.10
MA0090.10.315078
MA0091.14.82458
MA0092.10.253928
MA0093.10.429427
MA0095.10
MA0098.10
MA0100.10.00848234
MA0101.10.202458
MA0103.12.95427
MA0105.10.873098
MA0106.11.8863
MA0107.10.184108
MA0108.20.153582
MA0109.10
MA0111.10.729234
MA0113.10.0131846
MA0114.10.170544
MA0115.10.225497
MA0116.12.73028
MA0117.10.361412
MA0119.11.95159
MA0122.10.12468
MA0124.10.199604
MA0125.10.901279
MA0130.10
MA0131.10.0937354
MA0132.10
MA0133.10
MA0135.10.108976
MA0136.10.0410622
MA0139.10.257296
MA0140.10.744334
MA0141.12.10913
MA0142.10.0322914
MA0143.10.0132066
MA0144.10.407444
MA0145.12.29962
MA0146.11.45844
MA0147.11.86334
MA0148.10.401363
MA0149.10.294703
MA0062.20.00141772
MA0035.20.503876
MA0039.22.37574
MA0138.20.669054
MA0002.20.0330444
MA0137.20.364672
MA0104.21.33787
MA0047.20.280735
MA0112.24.26972
MA0065.20.707269
MA0150.10.182435
MA0151.10
MA0152.10.181511
MA0153.10.438955
MA0154.10.833951
MA0155.12.73018
MA0156.10.154454
MA0157.10.111415
MA0158.10
MA0159.10.132077
MA0160.10.145647
MA0161.10
MA0162.10.208172
MA0163.11.51019
MA0164.10.889456
MA0080.20.00348344
MA0018.20.150885
MA0099.20.00485301
MA0079.22.9114
MA0102.21.98068
MA0258.11.17081
MA0259.10.228583
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
SUZ12#2351294.465762655441250.0001995484019794490.00239575072471912



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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