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Coexpression cluster:C1941

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Full id: C1941_Fibroblast_Nucleus_Mesenchymal_tenocyte_Anulus_Smooth_acute



Phase1 CAGE Peaks

Hg19::chr4:55095379..55095390,+p6@PDGFRA
Hg19::chr4:55095396..55095422,+p3@PDGFRA
Hg19::chr4:55095428..55095475,+p2@PDGFRA
Hg19::chr4:55095476..55095494,+p4@PDGFRA
Hg19::chr4:55162545..55162559,+p@chr4:55162545..55162559
+


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
somite4.90e-1983
paraxial mesoderm4.90e-1983
presomitic mesoderm4.90e-1983
presumptive segmental plate4.90e-1983
trunk paraxial mesoderm4.90e-1983
presumptive paraxial mesoderm4.90e-1983
organism subdivision1.66e-17365
dermomyotome1.45e-1670
muscle tissue1.63e-1463
musculature1.63e-1463
musculature of body1.63e-1463
skeletal muscle tissue4.57e-1461
striated muscle tissue4.57e-1461
myotome4.57e-1461
multi-tissue structure1.79e-13347
multilaminar epithelium1.85e-1282
multi-cellular organism2.02e-12659
adult organism9.03e-12115
trunk mesenchyme4.62e-11143
surface structure2.58e-1095
primary circulatory organ1.83e-0927
heart2.36e-0924
primitive heart tube2.36e-0924
primary heart field2.36e-0924
anterior lateral plate mesoderm2.36e-0924
heart tube2.36e-0924
heart primordium2.36e-0924
cardiac mesoderm2.36e-0924
cardiogenic plate2.36e-0924
heart rudiment2.36e-0924
anatomical cluster5.68e-09286
anatomical group9.84e-09626
anatomical system1.11e-08625
integument1.74e-0845
integumental system1.74e-0845
splanchnic layer of lateral plate mesoderm3.55e-0884
cell layer4.90e-08312
epithelium1.01e-07309
trunk2.38e-07216
skin of body3.98e-0740
tissue6.14e-07787
anatomical conduit7.76e-07241


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
CEBPB#105146.376918100659850.001113944176677320.00765792626829925
EP300#203345.419153380978560.00209386927943890.0121254013681907
RAD21#588548.284027116365060.0004011622639122450.0038689616474957
YY1#752843.928936599883080.007193866269917620.0298545736058144



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.