Coexpression cluster:C2298

Full id: C2298_pagetoid_liposarcoma_mesothelioma_mucinous_epidermoid_large_bile

Phase1 CAGE Peaks

Hg19::chr14:52021357..52021368,+	p13@FRMD6
Hg19::chr14:52021378..52021407,+	p3@FRMD6
Hg19::chr14:52021408..52021419,+	p8@FRMD6
Hg19::chr14:52021434..52021439,+	p22@FRMD6

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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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>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	1.22e-33	180
fibroblast	8.76e-22	75
animal cell	7.36e-19	679
eukaryotic cell	7.36e-19	679
vascular associated smooth muscle cell	1.76e-15	32
muscle precursor cell	2.37e-15	57
myoblast	2.37e-15	57
multi-potent skeletal muscle stem cell	2.37e-15	57
smooth muscle cell	2.77e-15	42
smooth muscle myoblast	2.77e-15	42
muscle cell	7.65e-14	54
skin fibroblast	2.56e-13	23
mesodermal cell	3.04e-13	119
embryonic cell	1.13e-12	248
somatic cell	1.14e-12	591
contractile cell	1.25e-12	59
native cell	4.82e-12	722
electrically responsive cell	1.69e-11	60
electrically active cell	1.69e-11	60
aortic smooth muscle cell	2.42e-07	10

Uber Anatomy

Ontology term	p-value	n
somite	6.59e-19	83
paraxial mesoderm	6.59e-19	83
presomitic mesoderm	6.59e-19	83
presumptive segmental plate	6.59e-19	83
trunk paraxial mesoderm	6.59e-19	83
presumptive paraxial mesoderm	6.59e-19	83
trunk mesenchyme	1.57e-17	143
multilaminar epithelium	8.44e-16	82
dermomyotome	9.18e-16	70
skeletal muscle tissue	3.11e-13	61
striated muscle tissue	3.11e-13	61
myotome	3.11e-13	61
trunk	2.17e-12	216
muscle tissue	2.70e-12	63
musculature	2.70e-12	63
musculature of body	2.70e-12	63
surface structure	2.08e-11	95
organism subdivision	4.93e-11	365
unilaminar epithelium	1.75e-10	138
artery	1.98e-10	42
arterial blood vessel	1.98e-10	42
arterial system	1.98e-10	42
systemic artery	1.65e-09	33
systemic arterial system	1.65e-09	33
skin of body	2.82e-09	40
integument	3.10e-09	45
integumental system	3.10e-09	45
vasculature	4.31e-08	79
vascular system	4.31e-08	79
splanchnic layer of lateral plate mesoderm	8.22e-08	84
mesenchyme	9.28e-08	238
entire embryonic mesenchyme	9.28e-08	238
epithelial tube	1.00e-07	118
blood vessel	1.47e-07	60
epithelial tube open at both ends	1.47e-07	60
blood vasculature	1.47e-07	60
vascular cord	1.47e-07	60
blood vessel smooth muscle	2.42e-07	10
arterial system smooth muscle	2.42e-07	10
artery smooth muscle tissue	2.42e-07	10
aorta smooth muscle tissue	2.42e-07	10
vessel	9.65e-07	69

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)
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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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
EP300#2033	4	6.7739417262232	0.000474845982144264	0.00433689895314078
FOS#2353	4	8.9979553088944	0.000152514771116863	0.00194605866593452
JUN#3725	4	12.5128291923363	4.07770316866756e-05	0.000741935960335316
JUND#3727	4	6.99466394187103	0.00041768421781858	0.00391128145115706
PRDM1#639	4	131.830955777461	3.29673728703385e-09	2.72395526519405e-07

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.