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Coexpression cluster:C3565


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Full id: C3565_Hepatocyte_Mesenchymal_liver_Adipocyte_colon_Alveolar_Renal

Phase1 CAGE Peaks


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:0019754one-carbon compound catabolic process0.00153064978927681
GO:00086702,4-dienoyl-CoA reductase (NADPH) activity0.00153064978927681
GO:0009439cyanate metabolic process0.00153064978927681
GO:0009440cyanate catabolic process0.00153064978927681
GO:0004792thiosulfate sulfurtransferase activity0.00244896756971318
GO:0016783sulfurtransferase activity0.00306111934572935
GO:0016628oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor0.00699581431695691
GO:0008272sulfate transport0.0103280842914814
GO:0016782transferase activity, transferring sulfur-containing groups0.0210703285937496
GO:0016627oxidoreductase activity, acting on the CH-CH group of donors0.0235144913412218
GO:0044270nitrogen compound catabolic process0.0235144913412218
GO:0006730one-carbon compound metabolic process0.0338166342370627
GO:0031980mitochondrial lumen0.03492033499473
GO:0005759mitochondrial matrix0.03492033499473
GO:0015698inorganic anion transport0.0466420815271067
GO:0044444cytoplasmic part0.0480182555675481
GO:0005743mitochondrial inner membrane0.0480182555675481
GO:0006820anion transport0.0480182555675481
GO:0019866organelle inner membrane0.0480182555675481

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
entire embryonic mesenchyme2.48e-20238
epithelial tube8.49e-20118
trunk mesenchyme1.28e-19143
multi-tissue structure1.14e-17347
unilaminar epithelium1.38e-17138
vascular system3.13e-1379
multilaminar epithelium7.01e-1382
cell layer8.01e-13312
organism subdivision1.69e-12365
muscle tissue2.22e-1263
musculature of body2.22e-1263
skeletal muscle tissue3.53e-1261
striated muscle tissue3.53e-1261
subdivision of trunk6.64e-12113
paraxial mesoderm6.92e-1283
presomitic mesoderm6.92e-1283
presumptive segmental plate6.92e-1283
trunk paraxial mesoderm6.92e-1283
presumptive paraxial mesoderm6.92e-1283
splanchnic layer of lateral plate mesoderm2.18e-1084
anatomical cluster2.75e-10286
blood vessel3.66e-1060
epithelial tube open at both ends3.66e-1060
blood vasculature3.66e-1060
vascular cord3.66e-1060
endoderm-derived structure1.93e-09169
presumptive endoderm1.93e-09169
circulatory system1.94e-09113
multi-cellular organism3.85e-09659
cardiovascular system5.85e-09110
anatomical conduit6.51e-09241
abdominal segment of trunk1.24e-0861
arterial blood vessel1.35e-0842
arterial system1.35e-0842
subdivision of digestive tract4.78e-08129
endodermal part of digestive tract4.78e-08129
digestive system6.33e-08155
digestive tract6.33e-08155
primitive gut6.33e-08155
abdomen element1.55e-0755
abdominal segment element1.55e-0755
nephron epithelium2.44e-0716
uriniferous tubule2.44e-0716
metanephric mesenchyme2.44e-0716
nephrogenic mesenchyme2.44e-0716
excretory tube2.51e-0717
mesonephric epithelium2.51e-0717
mesonephric tubule2.51e-0717
nephric duct2.51e-0717
kidney epithelium2.51e-0717
renal duct2.51e-0717
mesonephric duct2.51e-0717
pronephric duct2.51e-0717
trunk region element2.79e-07107
mesoderm-derived structure3.69e-07448
presumptive mesoderm3.69e-07448
immaterial anatomical entity9.77e-07126

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



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.