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Coexpression cluster:C4565: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002049!5.67e-32!79;UBERON:0007798!5.67e-32!79;UBERON:0001009!1.76e-29!113;UBERON:0004535!1.12e-27!110;UBERON:0000119!6.12e-27!312;UBERON:0004872!1.47e-26!84;UBERON:0000055!1.17e-25!69;UBERON:0000483!2.54e-25!309;UBERON:0003914!3.12e-25!118;UBERON:0001981!3.36e-22!60;UBERON:0007500!3.36e-22!60;UBERON:0004537!3.36e-22!60;UBERON:0006965!3.36e-22!60;UBERON:0000025!1.16e-20!194;UBERON:0000490!3.97e-20!138;UBERON:0000477!2.99e-19!286;UBERON:0004111!9.94e-19!241;UBERON:0004290!1.57e-15!70;UBERON:0002385!2.07e-15!63;UBERON:0001015!2.07e-15!63;UBERON:0000383!2.07e-15!63;UBERON:0001134!5.36e-15!61;UBERON:0002036!5.36e-15!61;UBERON:0003082!5.36e-15!61;UBERON:0000475!1.99e-14!365;UBERON:0000481!7.39e-14!347;UBERON:0000914!1.92e-13!83;UBERON:0002329!1.92e-13!83;UBERON:0003077!1.92e-13!83;UBERON:0003059!1.92e-13!83;UBERON:0007282!1.92e-13!83;UBERON:0009618!1.92e-13!83;UBERON:0007285!1.92e-13!83;UBERON:0001637!3.29e-13!42;UBERON:0003509!3.29e-13!42;UBERON:0004572!3.29e-13!42;UBERON:0007100!4.88e-13!27;UBERON:0005256!1.14e-12!143;UBERON:0001986!1.27e-12!18;UBERON:0004638!1.27e-12!18;UBERON:0004852!1.27e-12!18;UBERON:0000468!2.18e-12!659;UBERON:0000486!3.10e-11!82;UBERON:0000948!3.30e-11!24;UBERON:0005498!3.30e-11!24;UBERON:0004140!3.30e-11!24;UBERON:0009881!3.30e-11!24;UBERON:0004141!3.30e-11!24;UBERON:0003084!3.30e-11!24;UBERON:0007005!3.30e-11!24;UBERON:0004139!3.30e-11!24;UBERON:0004291!3.30e-11!24;UBERON:0006914!3.49e-11!25;UBERON:0000487!4.87e-11!22;UBERON:0004573!8.25e-11!33;UBERON:0004571!8.25e-11!33;UBERON:0000467!2.22e-10!625;UBERON:0000480!3.41e-10!626;UBERON:0000947!3.96e-10!21;UBERON:0010191!3.96e-10!21;UBERON:0002100!4.42e-10!216;UBERON:0003103!3.28e-07!69;UBERON:0003915!6.80e-07!9;UBERON:0004700!6.80e-07!9;UBERON:0001917!6.80e-07!9
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}}
}}

Revision as of 20:08, 8 August 2012


Full id: C4565_heart_Meningeal_Endothelial_mesothelioma_Lymphatic_Renal_skeletal



Phase1 CAGE Peaks

Hg19::chr6:138866796..138866819,-p6@NHSL1
Hg19::chr6:138866823..138866851,-p3@NHSL1
Hg19::chr6:138866863..138866887,-p2@NHSL1


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
vasculature5.67e-3279
vascular system5.67e-3279
circulatory system1.76e-29113
cardiovascular system1.12e-27110
cell layer6.12e-27312
splanchnic layer of lateral plate mesoderm1.47e-2684
vessel1.17e-2569
epithelium2.54e-25309
epithelial tube3.12e-25118
blood vessel3.36e-2260
epithelial tube open at both ends3.36e-2260
blood vasculature3.36e-2260
vascular cord3.36e-2260
tube1.16e-20194
unilaminar epithelium3.97e-20138
anatomical cluster2.99e-19286
anatomical conduit9.94e-19241
dermomyotome1.57e-1570
muscle tissue2.07e-1563
musculature2.07e-1563
musculature of body2.07e-1563
skeletal muscle tissue5.36e-1561
striated muscle tissue5.36e-1561
myotome5.36e-1561
organism subdivision1.99e-14365
multi-tissue structure7.39e-14347
somite1.92e-1383
paraxial mesoderm1.92e-1383
presomitic mesoderm1.92e-1383
presumptive segmental plate1.92e-1383
trunk paraxial mesoderm1.92e-1383
presumptive paraxial mesoderm1.92e-1383
artery3.29e-1342
arterial blood vessel3.29e-1342
arterial system3.29e-1342
primary circulatory organ4.88e-1327
trunk mesenchyme1.14e-12143
endothelium1.27e-1218
blood vessel endothelium1.27e-1218
cardiovascular system endothelium1.27e-1218
multi-cellular organism2.18e-12659
multilaminar epithelium3.10e-1182
heart3.30e-1124
primitive heart tube3.30e-1124
primary heart field3.30e-1124
anterior lateral plate mesoderm3.30e-1124
heart tube3.30e-1124
heart primordium3.30e-1124
cardiac mesoderm3.30e-1124
cardiogenic plate3.30e-1124
heart rudiment3.30e-1124
squamous epithelium3.49e-1125
simple squamous epithelium4.87e-1122
systemic artery8.25e-1133
systemic arterial system8.25e-1133
anatomical system2.22e-10625
anatomical group3.41e-10626
aorta3.96e-1021
aortic system3.96e-1021
trunk4.42e-10216
compound organ3.28e-0769
endothelial tube6.80e-079
arterial system endothelium6.80e-079
endothelium of artery6.80e-079


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


This analysis result is provided for C0 - C305 clusters.