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Coexpression cluster:C2904

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Full id: C2904_Mesenchymal_adenocarcinoma_Cardiac_small_sacrococcigeal_Preadipocyte_Smooth



Phase1 CAGE Peaks

Hg19::chr7:81399311..81399323,-p6@HGF
Hg19::chr7:81399376..81399392,-p5@HGF
Hg19::chr7:81399411..81399432,-p4@HGF
Hg19::chr7:81399438..81399454,-p2@HGF


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
somite2.75e-2083
paraxial mesoderm2.75e-2083
presomitic mesoderm2.75e-2083
presumptive segmental plate2.75e-2083
trunk paraxial mesoderm2.75e-2083
presumptive paraxial mesoderm2.75e-2083
muscle tissue1.82e-1863
musculature1.82e-1863
musculature of body1.82e-1863
skeletal muscle tissue5.16e-1861
striated muscle tissue5.16e-1861
myotome5.16e-1861
dermomyotome9.54e-1870
musculoskeletal system2.27e-16167
adult organism5.17e-14115
multi-cellular organism9.63e-13659
trunk mesenchyme3.57e-12143
multilaminar epithelium4.47e-1282
tissue7.48e-12787
embryo3.88e-11612
embryonic structure6.56e-11605
developing anatomical structure6.56e-11605
anatomical system9.09e-11625
germ layer1.27e-10604
embryonic tissue1.27e-10604
presumptive structure1.27e-10604
epiblast (generic)1.27e-10604
anatomical group1.46e-10626
multi-tissue structure1.89e-10347
heart3.64e-1024
primitive heart tube3.64e-1024
primary heart field3.64e-1024
anterior lateral plate mesoderm3.64e-1024
heart tube3.64e-1024
heart primordium3.64e-1024
cardiac mesoderm3.64e-1024
cardiogenic plate3.64e-1024
heart rudiment3.64e-1024
primary circulatory organ8.83e-1027
splanchnic layer of lateral plate mesoderm3.99e-0984
anatomical cluster7.14e-09286
mesoderm7.59e-09448
mesoderm-derived structure7.59e-09448
presumptive mesoderm7.59e-09448
circulatory system9.34e-09113
cardiovascular system1.17e-08110
organism subdivision9.47e-08365
epithelium1.80e-07309
anatomical conduit2.03e-07241
unilaminar epithelium2.47e-07138
cell layer2.75e-07312
lateral plate mesoderm7.24e-07216
systemic artery9.24e-0733
systemic arterial system9.24e-0733


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
CTCF#1066445.360256373075030.001211145381643620.00819984522970818
RAD21#5885410.35503389545638.6948481184721e-050.00130004472819629



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.