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Coexpression cluster:C4565: Difference between revisions

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|tf_chipseq_enrich=REST#5978;3:9.65002871612802:0.00111263624711459:0.00770778833990453!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197885871208042!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191026754600277
|tf_chipseq_enrich=REST#5978;3:9.65002871612802:0.00111263624711459:0.00770778833990453!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197885871208042!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191026754600277
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}}
}}

Revision as of 16:49, 26 November 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
vasculature1.86e-3278
vascular system1.86e-3278
circulatory system4.76e-31112
cardiovascular system4.65e-29109
splanchnic layer of lateral plate mesoderm4.41e-2683
vessel4.54e-2668
cell layer8.35e-26309
epithelial tube3.01e-24117
epithelium3.62e-24306
epithelial tube open at both ends2.13e-2259
blood vessel2.13e-2259
blood vasculature2.13e-2259
vascular cord2.13e-2259
anatomical cluster1.19e-20373
unilaminar epithelium1.19e-20148
tube1.30e-19192
anatomical conduit7.24e-16240
epithelial vesicle1.37e-1578
dense mesenchyme tissue4.97e-1573
muscle tissue5.88e-1564
musculature5.88e-1564
musculature of body5.88e-1564
somite6.89e-1571
presomitic mesoderm6.89e-1571
presumptive segmental plate6.89e-1571
dermomyotome6.89e-1571
trunk paraxial mesoderm6.89e-1571
paraxial mesoderm6.91e-1572
presumptive paraxial mesoderm6.91e-1572
skeletal muscle tissue1.57e-1462
striated muscle tissue1.57e-1462
myotome1.57e-1462
trunk mesenchyme1.63e-13122
blood vessel endothelium2.11e-1318
endothelium2.11e-1318
cardiovascular system endothelium2.11e-1318
artery5.42e-1342
arterial blood vessel5.42e-1342
arterial system5.42e-1342
primary circulatory organ6.27e-1327
multi-tissue structure5.64e-12342
squamous epithelium2.05e-1125
multilaminar epithelium3.30e-1183
simple squamous epithelium3.86e-1122
multi-cellular organism5.01e-11656
heart6.33e-1124
primitive heart tube6.33e-1124
primary heart field6.33e-1124
anterior lateral plate mesoderm6.33e-1124
heart tube6.33e-1124
heart primordium6.33e-1124
cardiac mesoderm6.33e-1124
cardiogenic plate6.33e-1124
heart rudiment6.33e-1124
mesenchyme6.51e-11160
entire embryonic mesenchyme6.51e-11160
aorta1.20e-1021
aortic system1.20e-1021
systemic artery2.64e-1033
systemic arterial system2.64e-1033
structure with developmental contribution from neural crest2.96e-10132
anatomical system2.76e-09624
anatomical group3.92e-09625
organism subdivision8.20e-09264
trunk4.20e-08199
germ layer1.16e-07560
germ layer / neural crest1.16e-07560
embryonic tissue1.16e-07560
presumptive structure1.16e-07560
germ layer / neural crest derived structure1.16e-07560
epiblast (generic)1.16e-07560
embryonic structure1.74e-07564
endothelial tube2.51e-079
arterial system endothelium2.51e-079
endothelium of artery2.51e-079
primordium4.92e-07160


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
REST#597839.650028716128020.001112636247114590.00770778833990453
TRIM28#10155318.59052504526250.0001555969297255280.00197885871208042
USF1#739136.361499277207960.00388404057290560.0191026754600277



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.

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