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Coexpression cluster:C628: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000486!1.33e-13!82;UBERON:0002385!2.15e-13!63;UBERON:0001015!2.15e-13!63;UBERON:0000383!2.15e-13!63;UBERON:0004290!3.77e-13!70;UBERON:0001134!4.98e-13!61;UBERON:0002036!4.98e-13!61;UBERON:0003082!4.98e-13!61;UBERON:0000914!5.96e-13!83;UBERON:0002329!5.96e-13!83;UBERON:0003077!5.96e-13!83;UBERON:0003059!5.96e-13!83;UBERON:0007282!5.96e-13!83;UBERON:0009618!5.96e-13!83;UBERON:0007285!5.96e-13!83;UBERON:0004872!7.77e-12!84;UBERON:0000468!2.50e-10!659;UBERON:0001637!3.51e-10!42;UBERON:0003509!3.51e-10!42;UBERON:0004572!3.51e-10!42;UBERON:0004573!4.47e-10!33;UBERON:0004571!4.47e-10!33;UBERON:0000467!3.54e-09!625;UBERON:0000480!5.57e-09!626;UBERON:0000475!7.50e-09!365;UBERON:0004923!1.66e-08!57;UBERON:0007100!4.01e-08!27;UBERON:0005631!5.80e-08!14;UBERON:0000158!5.80e-08!14;UBERON:0002199!9.55e-08!45;UBERON:0002416!9.55e-08!45;UBERON:0000948!1.78e-07!24;UBERON:0005498!1.78e-07!24;UBERON:0004140!1.78e-07!24;UBERON:0009881!1.78e-07!24;UBERON:0004141!1.78e-07!24;UBERON:0003084!1.78e-07!24;UBERON:0007005!1.78e-07!24;UBERON:0004139!1.78e-07!24;UBERON:0004291!1.78e-07!24;UBERON:0003133!1.95e-07!48;UBERON:0005156!6.01e-07!59;UBERON:0000990!6.01e-07!59;UBERON:0005256!6.39e-07!143;UBERON:0001981!6.52e-07!60;UBERON:0007500!6.52e-07!60;UBERON:0004537!6.52e-07!60;UBERON:0006965!6.52e-07!60;UBERON:0002100!7.59e-07!216;UBERON:0003102!8.07e-07!95
|ontology_enrichment_uberon=UBERON:0000486!1.33e-13!82;UBERON:0002385!2.15e-13!63;UBERON:0001015!2.15e-13!63;UBERON:0000383!2.15e-13!63;UBERON:0004290!3.77e-13!70;UBERON:0001134!4.98e-13!61;UBERON:0002036!4.98e-13!61;UBERON:0003082!4.98e-13!61;UBERON:0000914!5.96e-13!83;UBERON:0002329!5.96e-13!83;UBERON:0003077!5.96e-13!83;UBERON:0003059!5.96e-13!83;UBERON:0007282!5.96e-13!83;UBERON:0009618!5.96e-13!83;UBERON:0007285!5.96e-13!83;UBERON:0004872!7.77e-12!84;UBERON:0000468!2.50e-10!659;UBERON:0001637!3.51e-10!42;UBERON:0003509!3.51e-10!42;UBERON:0004572!3.51e-10!42;UBERON:0004573!4.47e-10!33;UBERON:0004571!4.47e-10!33;UBERON:0000467!3.54e-09!625;UBERON:0000480!5.57e-09!626;UBERON:0000475!7.50e-09!365;UBERON:0004923!1.66e-08!57;UBERON:0007100!4.01e-08!27;UBERON:0005631!5.80e-08!14;UBERON:0000158!5.80e-08!14;UBERON:0002199!9.55e-08!45;UBERON:0002416!9.55e-08!45;UBERON:0000948!1.78e-07!24;UBERON:0005498!1.78e-07!24;UBERON:0004140!1.78e-07!24;UBERON:0009881!1.78e-07!24;UBERON:0004141!1.78e-07!24;UBERON:0003084!1.78e-07!24;UBERON:0007005!1.78e-07!24;UBERON:0004139!1.78e-07!24;UBERON:0004291!1.78e-07!24;UBERON:0003133!1.95e-07!48;UBERON:0005156!6.01e-07!59;UBERON:0000990!6.01e-07!59;UBERON:0005256!6.39e-07!143;UBERON:0001981!6.52e-07!60;UBERON:0007500!6.52e-07!60;UBERON:0004537!6.52e-07!60;UBERON:0006965!6.52e-07!60;UBERON:0002100!7.59e-07!216;UBERON:0003102!8.07e-07!95
|tf_chipseq_enrich=GTF2F1#2962;5:4.5498788845563:0.00326074959137569:0.0168873066832136!STAT3#6774;5:3.75695178469794:0.00745070695195861:0.0307360423176366
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}}
}}

Revision as of 12:57, 5 September 2012


Full id: C628_Adipocyte_Preadipocyte_Fibroblast_tenocyte_Smooth_Placental_chorionic



Phase1 CAGE Peaks

Hg19::chr12:8798930..8798945,-p@chr12:8798930..8798945
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Hg19::chr12:8798958..8798980,-p@chr12:8798958..8798980
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Hg19::chr12:8799724..8799753,-p9@MFAP5
Hg19::chr12:8800547..8800576,-p8@MFAP5
Hg19::chr12:8800599..8800615,-p10@MFAP5
Hg19::chr12:8800619..8800651,-p6@MFAP5
Hg19::chr12:8800745..8800781,-p@chr12:8800745..8800781
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Hg19::chr12:8803128..8803164,-p7@MFAP5
Hg19::chr12:8815259..8815298,-p2@MFAP5
Hg19::chr12:8815299..8815331,-p3@MFAP5
Hg19::chr12:8815363..8815398,-p4@MFAP5
Hg19::chr12:8815404..8815438,-p1@MFAP5
Hg19::chr12:8815477..8815490,-p5@MFAP5
Hg19::chr3:112321809..112321819,-p@chr3:112321809..112321819
-


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


No GOStat results

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
multilaminar epithelium1.33e-1382
muscle tissue2.15e-1363
musculature2.15e-1363
musculature of body2.15e-1363
dermomyotome3.77e-1370
skeletal muscle tissue4.98e-1361
striated muscle tissue4.98e-1361
myotome4.98e-1361
somite5.96e-1383
paraxial mesoderm5.96e-1383
presomitic mesoderm5.96e-1383
presumptive segmental plate5.96e-1383
trunk paraxial mesoderm5.96e-1383
presumptive paraxial mesoderm5.96e-1383
splanchnic layer of lateral plate mesoderm7.77e-1284
multi-cellular organism2.50e-10659
artery3.51e-1042
arterial blood vessel3.51e-1042
arterial system3.51e-1042
systemic artery4.47e-1033
systemic arterial system4.47e-1033
anatomical system3.54e-09625
anatomical group5.57e-09626
organism subdivision7.50e-09365
organ component layer1.66e-0857
primary circulatory organ4.01e-0827
extraembryonic membrane5.80e-0814
membranous layer5.80e-0814
integument9.55e-0845
integumental system9.55e-0845
heart1.78e-0724
primitive heart tube1.78e-0724
primary heart field1.78e-0724
anterior lateral plate mesoderm1.78e-0724
heart tube1.78e-0724
heart primordium1.78e-0724
cardiac mesoderm1.78e-0724
cardiogenic plate1.78e-0724
heart rudiment1.78e-0724
reproductive organ1.95e-0748
reproductive structure6.01e-0759
reproductive system6.01e-0759
trunk mesenchyme6.39e-07143
blood vessel6.52e-0760
epithelial tube open at both ends6.52e-0760
blood vasculature6.52e-0760
vascular cord6.52e-0760
trunk7.59e-07216
surface structure8.07e-0795


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
GTF2F1#296254.54987888455630.003260749591375690.0168873066832136
STAT3#677453.756951784697940.007450706951958610.0307360423176366



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


This analysis result is provided for C0 - C305 clusters.