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Coexpression cluster:C4394: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004872!1.39e-18!84;UBERON:0002385!4.60e-15!63;UBERON:0001015!4.60e-15!63;UBERON:0000383!4.60e-15!63;UBERON:0007100!1.06e-14!27;UBERON:0001134!6.32e-14!61;UBERON:0002036!6.32e-14!61;UBERON:0003082!6.32e-14!61;UBERON:0004290!2.04e-13!70;UBERON:0000948!1.64e-12!24;UBERON:0005498!1.64e-12!24;UBERON:0004140!1.64e-12!24;UBERON:0009881!1.64e-12!24;UBERON:0004141!1.64e-12!24;UBERON:0003084!1.64e-12!24;UBERON:0007005!1.64e-12!24;UBERON:0004139!1.64e-12!24;UBERON:0004291!1.64e-12!24;UBERON:0000914!7.31e-11!83;UBERON:0002329!7.31e-11!83;UBERON:0003077!7.31e-11!83;UBERON:0003059!7.31e-11!83;UBERON:0007282!7.31e-11!83;UBERON:0009618!7.31e-11!83;UBERON:0007285!7.31e-11!83;UBERON:0000478!7.42e-11!24;UBERON:0001637!8.37e-11!42;UBERON:0003509!8.37e-11!42;UBERON:0004572!8.37e-11!42;UBERON:0001009!1.06e-10!113;UBERON:0003914!1.91e-10!118;UBERON:0000486!1.99e-10!82;UBERON:0001981!2.44e-10!60;UBERON:0007500!2.44e-10!60;UBERON:0004537!2.44e-10!60;UBERON:0006965!2.44e-10!60;UBERON:0004535!2.16e-09!110;UBERON:0000468!3.96e-09!659;UBERON:0005631!1.06e-08!14;UBERON:0000158!1.06e-08!14;UBERON:0004573!3.54e-08!33;UBERON:0004571!3.54e-08!33;UBERON:0000055!4.24e-08!69;UBERON:0004923!4.86e-08!57;UBERON:0002049!2.15e-07!79;UBERON:0007798!2.15e-07!79;UBERON:0002100!2.54e-07!216;UBERON:0005256!2.65e-07!143
|ontology_enrichment_uberon=UBERON:0004872!1.39e-18!84;UBERON:0002385!4.60e-15!63;UBERON:0001015!4.60e-15!63;UBERON:0000383!4.60e-15!63;UBERON:0007100!1.06e-14!27;UBERON:0001134!6.32e-14!61;UBERON:0002036!6.32e-14!61;UBERON:0003082!6.32e-14!61;UBERON:0004290!2.04e-13!70;UBERON:0000948!1.64e-12!24;UBERON:0005498!1.64e-12!24;UBERON:0004140!1.64e-12!24;UBERON:0009881!1.64e-12!24;UBERON:0004141!1.64e-12!24;UBERON:0003084!1.64e-12!24;UBERON:0007005!1.64e-12!24;UBERON:0004139!1.64e-12!24;UBERON:0004291!1.64e-12!24;UBERON:0000914!7.31e-11!83;UBERON:0002329!7.31e-11!83;UBERON:0003077!7.31e-11!83;UBERON:0003059!7.31e-11!83;UBERON:0007282!7.31e-11!83;UBERON:0009618!7.31e-11!83;UBERON:0007285!7.31e-11!83;UBERON:0000478!7.42e-11!24;UBERON:0001637!8.37e-11!42;UBERON:0003509!8.37e-11!42;UBERON:0004572!8.37e-11!42;UBERON:0001009!1.06e-10!113;UBERON:0003914!1.91e-10!118;UBERON:0000486!1.99e-10!82;UBERON:0001981!2.44e-10!60;UBERON:0007500!2.44e-10!60;UBERON:0004537!2.44e-10!60;UBERON:0006965!2.44e-10!60;UBERON:0004535!2.16e-09!110;UBERON:0000468!3.96e-09!659;UBERON:0005631!1.06e-08!14;UBERON:0000158!1.06e-08!14;UBERON:0004573!3.54e-08!33;UBERON:0004571!3.54e-08!33;UBERON:0000055!4.24e-08!69;UBERON:0004923!4.86e-08!57;UBERON:0002049!2.15e-07!79;UBERON:0007798!2.15e-07!79;UBERON:0002100!2.54e-07!216;UBERON:0005256!2.65e-07!143
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168059518058296!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330614698283624
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}}
}}

Revision as of 13:51, 5 September 2012


Full id: C4394_neuroblastoma_Mesenchymal_rectum_heart_neuroectodermal_leiomyoma_gall



Phase1 CAGE Peaks

Hg19::chr4:174451350..174451363,-p3@HAND2
Hg19::chr4:174451370..174451387,-p1@HAND2
Hg19::chr4:174451596..174451632,+p1@NBLA00301


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:0007507heart development0.038276619961537
GO:0001525angiogenesis0.038276619961537
GO:0048514blood vessel morphogenesis0.038276619961537
GO:0048646anatomical structure formation0.038276619961537
GO:0001568blood vessel development0.038276619961537
GO:0001944vasculature development0.038276619961537



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
splanchnic layer of lateral plate mesoderm1.39e-1884
muscle tissue4.60e-1563
musculature4.60e-1563
musculature of body4.60e-1563
primary circulatory organ1.06e-1427
skeletal muscle tissue6.32e-1461
striated muscle tissue6.32e-1461
myotome6.32e-1461
dermomyotome2.04e-1370
heart1.64e-1224
primitive heart tube1.64e-1224
primary heart field1.64e-1224
anterior lateral plate mesoderm1.64e-1224
heart tube1.64e-1224
heart primordium1.64e-1224
cardiac mesoderm1.64e-1224
cardiogenic plate1.64e-1224
heart rudiment1.64e-1224
somite7.31e-1183
paraxial mesoderm7.31e-1183
presomitic mesoderm7.31e-1183
presumptive segmental plate7.31e-1183
trunk paraxial mesoderm7.31e-1183
presumptive paraxial mesoderm7.31e-1183
extraembryonic structure7.42e-1124
artery8.37e-1142
arterial blood vessel8.37e-1142
arterial system8.37e-1142
circulatory system1.06e-10113
epithelial tube1.91e-10118
multilaminar epithelium1.99e-1082
blood vessel2.44e-1060
epithelial tube open at both ends2.44e-1060
blood vasculature2.44e-1060
vascular cord2.44e-1060
cardiovascular system2.16e-09110
multi-cellular organism3.96e-09659
extraembryonic membrane1.06e-0814
membranous layer1.06e-0814
systemic artery3.54e-0833
systemic arterial system3.54e-0833
vessel4.24e-0869
organ component layer4.86e-0857
vasculature2.15e-0779
vascular system2.15e-0779
trunk2.54e-07216
trunk mesenchyme2.65e-07143


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)

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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
EP300#203336.77394172622320.003216880500103790.0168059518058296
YY1#752834.911170749853860.008441455341808260.0330614698283624



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.