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Coexpression cluster:C4394: Difference between revisions

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|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168059518058296!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330614698283624
|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 16:43, 26 November 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 mesoderm1.32e-1683
primary circulatory organ8.45e-1627
heart3.28e-1324
primitive heart tube3.28e-1324
primary heart field3.28e-1324
anterior lateral plate mesoderm3.28e-1324
heart tube3.28e-1324
heart primordium3.28e-1324
cardiac mesoderm3.28e-1324
cardiogenic plate3.28e-1324
heart rudiment3.28e-1324
extraembryonic structure1.52e-1224
muscle tissue2.85e-1164
musculature2.85e-1164
musculature of body2.85e-1164
epithelial tube2.54e-10117
skeletal muscle tissue3.67e-1062
striated muscle tissue3.67e-1062
myotome3.67e-1062
somite5.90e-1071
presomitic mesoderm5.90e-1071
presumptive segmental plate5.90e-1071
dermomyotome5.90e-1071
trunk paraxial mesoderm5.90e-1071
mesoderm6.14e-10315
mesoderm-derived structure6.14e-10315
presumptive mesoderm6.14e-10315
circulatory system6.96e-10112
paraxial mesoderm1.27e-0972
presumptive paraxial mesoderm1.27e-0972
extraembryonic membrane1.95e-0914
membranous layer1.95e-0914
artery2.08e-0942
arterial blood vessel2.08e-0942
arterial system2.08e-0942
dense mesenchyme tissue2.66e-0973
multi-cellular organism3.36e-09656
mesenchyme7.15e-09160
entire embryonic mesenchyme7.15e-09160
epithelial tube open at both ends8.08e-0959
blood vessel8.08e-0959
blood vasculature8.08e-0959
vascular cord8.08e-0959
cardiovascular system1.76e-08109
trunk mesenchyme2.40e-08122
epithelial vesicle7.49e-0878
multilaminar epithelium1.39e-0783
systemic artery6.99e-0733
systemic arterial system6.99e-0733
vessel9.22e-0768
organ component layer9.51e-0766


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.