Coexpression cluster:C1002

Full id: C1002_Mesenchymal_Whole_Smooth_Renal_osteosarcoma_Fibroblast_Reticulocytes

Phase1 CAGE Peaks

Hg19::chr11:66367106..66367110,+	p4@CCS
Hg19::chr12:49717819..49717823,+	p@chr12:49717819..49717823 +
Hg19::chr17:5284799..5284803,+	p@chr17:5284799..5284803 +
Hg19::chr1:149897719..149897733,-	p@chr1:149897719..149897733 -
Hg19::chr1:156223236..156223240,-	p4@SMG5
Hg19::chr1:45471462..45471466,-	p2@HECTD3
Hg19::chr20:44586221..44586225,-	p@chr20:44586221..44586225 -
Hg19::chr20:44983518..44983521,-	p@chr20:44983518..44983521 -

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0015680	intracellular copper ion transport	0.0112151183327446
GO:0051721	protein phosphatase 2A binding	0.0129779004996243
GO:0051353	positive regulation of oxidoreductase activity	0.0129779004996243
GO:0035303	regulation of dephosphorylation	0.0129779004996243
GO:0004785	copper, zinc superoxide dismutase activity	0.0129779004996243
GO:0016721	oxidoreductase activity, acting on superoxide radicals as acceptor	0.0129779004996243
GO:0004784	superoxide dismutase activity	0.0129779004996243
GO:0030071	regulation of mitotic metaphase/anaphase transition	0.0129779004996243
GO:0007091	mitotic metaphase/anaphase transition	0.0129779004996243
GO:0051341	regulation of oxidoreductase activity	0.0129779004996243
GO:0005375	copper ion transmembrane transporter activity	0.0129779004996243
GO:0019903	protein phosphatase binding	0.0129779004996243
GO:0005680	anaphase-promoting complex	0.0129779004996243
GO:0006825	copper ion transport	0.0129779004996243
GO:0006801	superoxide metabolic process	0.0129779004996243
GO:0000184	mRNA catabolic process, nonsense-mediated decay	0.0129779004996243
GO:0000152	nuclear ubiquitin ligase complex	0.0129779004996243
GO:0006406	mRNA export from nucleus	0.0129779004996243
GO:0019902	phosphatase binding	0.0129779004996243
GO:0046907	intracellular transport	0.0134110274761918
GO:0006402	mRNA catabolic process	0.0146159308186139
GO:0046915	transition metal ion transmembrane transporter activity	0.0146159308186139
GO:0006405	RNA export from nucleus	0.0146159308186139
GO:0051649	establishment of cellular localization	0.0162125008845377
GO:0051641	cellular localization	0.0163590933226291
GO:0051168	nuclear export	0.0184004411671435
GO:0006800	oxygen and reactive oxygen species metabolic process	0.0184004411671435
GO:0006401	RNA catabolic process	0.0184004411671435
GO:0015082	di-, tri-valent inorganic cation transmembrane transporter activity	0.020850759210351
GO:0005634	nucleus	0.0234028841151839
GO:0007088	regulation of mitosis	0.0234028841151839
GO:0051174	regulation of phosphorus metabolic process	0.0234028841151839
GO:0019220	regulation of phosphate metabolic process	0.0234028841151839
GO:0051028	mRNA transport	0.0257257353024162
GO:0000151	ubiquitin ligase complex	0.0257257353024162
GO:0065007	biological regulation	0.0257257353024162
GO:0050658	RNA transport	0.0257257353024162
GO:0051236	establishment of RNA localization	0.0257257353024162
GO:0050657	nucleic acid transport	0.0257257353024162
GO:0006403	RNA localization	0.0257257353024162
GO:0000041	transition metal ion transport	0.027686652566795
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.027686652566795
GO:0005507	copper ion binding	0.0304114713492289
GO:0006913	nucleocytoplasmic transport	0.0387019507964772
GO:0051169	nuclear transport	0.0387019507964772
GO:0004842	ubiquitin-protein ligase activity	0.0394187598909581
GO:0008639	small protein conjugating enzyme activity	0.0394187598909581
GO:0043231	intracellular membrane-bound organelle	0.0454542410847666
GO:0043227	membrane-bound organelle	0.0454542410847666
GO:0005515	protein binding	0.0472949942100303

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>

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Cell Type

Ontology term	p-value	n
native cell	6.00e-21	722
animal cell	6.31e-19	679
eukaryotic cell	6.31e-19	679
somatic cell	2.49e-16	591
non-terminally differentiated cell	8.04e-15	180
embryonic cell	1.75e-11	248
contractile cell	2.25e-09	59
mesodermal cell	3.10e-08	119
muscle precursor cell	3.34e-08	57
myoblast	3.34e-08	57
multi-potent skeletal muscle stem cell	3.34e-08	57
electrically responsive cell	5.48e-08	60
electrically active cell	5.48e-08	60
muscle cell	7.31e-08	54
epithelial cell	6.87e-07	254

Uber Anatomy

Ontology term	p-value	n
cardiovascular system	4.57e-11	110
unilaminar epithelium	8.66e-11	138
circulatory system	6.83e-10	113
multilaminar epithelium	6.60e-09	82
trunk mesenchyme	1.46e-08	143
dermomyotome	5.85e-08	70
somite	9.42e-08	83
paraxial mesoderm	9.42e-08	83
presomitic mesoderm	9.42e-08	83
presumptive segmental plate	9.42e-08	83
trunk paraxial mesoderm	9.42e-08	83
presumptive paraxial mesoderm	9.42e-08	83
vasculature	1.75e-07	79
vascular system	1.75e-07	79
trunk	3.14e-07	216
mesenchyme	4.97e-07	238
entire embryonic mesenchyme	4.97e-07	238
skeletal muscle tissue	6.74e-07	61
striated muscle tissue	6.74e-07	61
myotome	6.74e-07	61

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

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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

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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

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This analysis result is provided for C0 - C305 clusters.