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Coexpression cluster:C1751: Difference between revisions

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|tf_chipseq_enrich=EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110793794348814
|tf_chipseq_enrich=EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110793794348814
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}}
}}

Revision as of 15:04, 26 November 2012


Full id: C1751_Mesenchymal_Fibroblast_tenocyte_Smooth_Synoviocyte_Hair_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr15:74466034..74466097,+p2@ISLR
Hg19::chr15:74466124..74466168,+p3@ISLR
Hg19::chr15:74466169..74466212,+p4@ISLR
Hg19::chr15:74466233..74466257,+p5@ISLR
Hg19::chr15:74466268..74466273,+p10@ISLR


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
adult organism4.03e-16114
dense mesenchyme tissue1.85e-1373
paraxial mesoderm1.92e-1372
presumptive paraxial mesoderm1.92e-1372
muscle tissue2.66e-1364
musculature2.66e-1364
musculature of body2.66e-1364
somite3.39e-1371
presomitic mesoderm3.39e-1371
presumptive segmental plate3.39e-1371
dermomyotome3.39e-1371
trunk paraxial mesoderm3.39e-1371
tissue1.08e-12773
skeletal muscle tissue1.37e-1262
striated muscle tissue1.37e-1262
myotome1.37e-1262
epithelial vesicle2.76e-1078
multilaminar epithelium3.14e-1083
multi-tissue structure5.49e-10342
multi-cellular organism2.76e-09656
structure with developmental contribution from neural crest6.42e-09132
adipose tissue1.41e-0814
primary circulatory organ4.03e-0827
trunk mesenchyme5.60e-08122
integument1.46e-0746
integumental system1.46e-0746
heart1.87e-0724
primitive heart tube1.87e-0724
primary heart field1.87e-0724
anterior lateral plate mesoderm1.87e-0724
heart tube1.87e-0724
heart primordium1.87e-0724
cardiac mesoderm1.87e-0724
cardiogenic plate1.87e-0724
heart rudiment1.87e-0724
anatomical group2.56e-07625
mesenchyme2.70e-07160
entire embryonic mesenchyme2.70e-07160
anatomical system3.47e-07624
splanchnic layer of lateral plate mesoderm5.31e-0783


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
EP300#203356.77394172622327.00901578206049e-050.00110793794348814



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.