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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C171_merkel_neuroblastoma_pineal_retinoblastoma_carcinoid_small_eye
|full_id=C171_merkel_neuroblastoma_pineal_retinoblastoma_carcinoid_small_eye
|gostat_on_coexpression_clusters=GO:0007275!multicellular organismal development!0.000641210868674468!120237;7399;644168;2313;10677;7163;4807;8022$GO:0032502!developmental process!0.000641210868674468!7399;644168;2313;10677;8022;120237;7161;4807;7163$GO:0048856!anatomical structure development!0.00144825555041831!7161;7399;2313;10677;7163;4807;8022$GO:0043565!sequence-specific DNA binding!0.00197243719679013!120237;340260;644168;2313;8022$GO:0003700!transcription factor activity!0.00197243719679013!7161;120237;340260;644168;2313;8022$GO:0048731!system development!0.00241078521397418!7399;2313;10677;7163;4807;8022$GO:0044424!intracellular part!0.00438791712875587!92369;7399;114780;644168;2313;10677;445;8022;120237;7161;340260;56683;7163;4807$GO:0032501!multicellular organismal process!0.00438791712875587!120237;7399;644168;2313;10677;7163;4807;8022$GO:0019222!regulation of metabolic process!0.00699071498393437!7161;120237;340260;644168;2313;10677;4807;8022$GO:0050794!regulation of cellular process!0.00955040933301972!7399;644168;2313;10677;8022;120237;7161;340260;4807$GO:0006355!regulation of transcription, DNA-dependent!0.0103851039816391!7161;120237;340260;644168;2313;4807;8022$GO:0006351!transcription, DNA-dependent!0.0103851039816391!7161;120237;340260;644168;2313;4807;8022$GO:0032774!RNA biosynthetic process!0.0103851039816391!7161;120237;340260;644168;2313;4807;8022$GO:0003677!DNA binding!0.010758642121758!7161;120237;340260;644168;2313;4807;8022$GO:0050789!regulation of biological process!0.0112451306537117!7399;644168;2313;10677;8022;120237;7161;340260;4807$GO:0045449!regulation of transcription!0.0118718949045196!7161;120237;340260;644168;2313;4807;8022$GO:0065008!regulation of biological quality!0.0118718949045196!7161;7399;2313;10677$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0118718949045196!7161;120237;340260;644168;2313;4807;8022$GO:0006350!transcription!0.0128681907351291!7161;120237;340260;644168;2313;4807;8022$GO:0010468!regulation of gene expression!0.0128681907351291!7161;120237;340260;644168;2313;4807;8022$GO:0005622!intracellular!0.0128681907351291!92369;7399;114780;644168;2313;10677;445;8022;120237;7161;340260;56683;7163;4807$GO:0009653!anatomical structure morphogenesis!0.0131530478983111!7161;2313;7163;8022$GO:0031323!regulation of cellular metabolic process!0.0131530478983111!7161;120237;340260;644168;2313;4807;8022$GO:0065007!biological regulation!0.0141190093803605!7399;644168;2313;10677;8022;120237;7161;340260;4807$GO:0048513!organ development!0.0161555509443677!7399;2313;7163;8022$GO:0016070!RNA metabolic process!0.0161555509443677!7161;120237;340260;644168;2313;4807;8022$GO:0048496!maintenance of organ identity!0.0172228248639993!7399$GO:0002347!response to tumor cell!0.0249005894688049!7161$GO:0005634!nucleus!0.0284863001369077!7161;120237;340260;644168;56683;2313;4807;8022$GO:0043603!amide metabolic process!0.0290378655176246!445$GO:0019627!urea metabolic process!0.0290378655176246!445$GO:0000050!urea cycle!0.0290378655176246!445$GO:0004055!argininosuccinate synthase activity!0.0316706804307545!445$GO:0044464!cell part!0.0447072753794081!92369;114780;2313;445;8022;7161;9080;4807;7399;644168;9378;10677;120237;340260;56683;7163$GO:0045494!photoreceptor cell maintenance!0.0497023599078022!7399
|id=C171
|id=C171
}}
}}

Revision as of 17:35, 18 May 2012


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>disease_data<br>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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

No analysis results for this cluster

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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

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