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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1421_Mesenchymal_Preadipocyte_Fibroblast_tenocyte_Adipocyte_Osteoblast_Nucleus
|full_id=C1421_Mesenchymal_Preadipocyte_Fibroblast_tenocyte_Adipocyte_Osteoblast_Nucleus
|gostat_on_coexpression_clusters=GO:0005578!proteinaceous extracellular matrix!0.0118525173614682!1292;79883$GO:0044421!extracellular region part!0.0274556468016525!1292;79883$GO:0030198!extracellular matrix organization and biogenesis!0.0351588482143845!1292$GO:0043062!extracellular structure organization and biogenesis!0.041676742962934!1292$GO:0030674!protein binding, bridging!0.041676742962934!1292$GO:0005201!extracellular matrix structural constituent!0.0467083833212877!1292$GO:0006817!phosphate transport!0.0467083833212877!1292
|gostat_on_coexpression_clusters=GO:0005578!proteinaceous extracellular matrix!0.0118525173614682!1292;79883$GO:0044421!extracellular region part!0.0274556468016525!1292;79883$GO:0030198!extracellular matrix organization and biogenesis!0.0351588482143845!1292$GO:0043062!extracellular structure organization and biogenesis!0.041676742962934!1292$GO:0030674!protein binding, bridging!0.041676742962934!1292$GO:0005201!extracellular matrix structural constituent!0.0467083833212877!1292$GO:0006817!phosphate transport!0.0467083833212877!1292

Revision as of 13:58, 12 September 2012


Full id: C1421_Mesenchymal_Preadipocyte_Fibroblast_tenocyte_Adipocyte_Osteoblast_Nucleus



Phase1 CAGE Peaks

Hg19::chr16:4431722..4431771,+p@chr16:4431722..4431771
+
Hg19::chr19:14049136..14049171,-p2@PODNL1
Hg19::chr19:14049184..14049242,-p1@PODNL1
Hg19::chr1:1290954..1290971,-p8@MXRA8
Hg19::chr1:1293904..1293949,-p1@MXRA8
Hg19::chr21:47517478..47517529,+p9@COL6A2


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


GO IDGO nameFDR corrected p-value
GO:0005578proteinaceous extracellular matrix0.0118525173614682
GO:0044421extracellular region part0.0274556468016525
GO:0030198extracellular matrix organization and biogenesis0.0351588482143845
GO:0043062extracellular structure organization and biogenesis0.041676742962934
GO:0030674protein binding, bridging0.041676742962934
GO:0005201extracellular matrix structural constituent0.0467083833212877
GO:0006817phosphate transport0.0467083833212877



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
organism subdivision4.40e-24365
somite1.21e-2283
paraxial mesoderm1.21e-2283
presomitic mesoderm1.21e-2283
presumptive segmental plate1.21e-2283
trunk paraxial mesoderm1.21e-2283
presumptive paraxial mesoderm1.21e-2283
trunk mesenchyme6.19e-20143
dermomyotome6.30e-2070
muscle tissue1.36e-1763
musculature1.36e-1763
musculature of body1.36e-1763
skeletal muscle tissue1.55e-1761
striated muscle tissue1.55e-1761
myotome1.55e-1761
multilaminar epithelium3.31e-1782
multi-tissue structure1.74e-16347
trunk1.33e-15216
multi-cellular organism1.27e-12659
surface structure2.36e-1095
mesenchyme2.83e-10238
entire embryonic mesenchyme2.83e-10238
cell layer8.91e-10312
epithelium1.48e-09309
integument9.86e-0945
integumental system9.86e-0945
organ component layer1.36e-0857
anatomical system1.98e-08625
anatomical group3.25e-08626
tissue1.88e-07787
adipose tissue3.71e-0714
skin of body6.78e-0740


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.