Coexpression cluster:C2994

Full id: C2994_osteosarcoma_Fibroblast_mesodermal_Wilms_fibrous_Lymphatic_neuroectodermal

Phase1 CAGE Peaks

Hg19::chr10:14050416..14050460,-	p5@FRMD4A
Hg19::chr10:14050463..14050515,-	p4@FRMD4A
Hg19::chr10:14050522..14050584,-	p3@FRMD4A

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
mesodermal cell	1.66e-15	119
non-terminally differentiated cell	1.68e-13	180
contractile cell	3.17e-12	59
smooth muscle cell	6.22e-12	42
smooth muscle myoblast	6.22e-12	42
vascular associated smooth muscle cell	7.16e-12	32
muscle cell	8.55e-12	54
muscle precursor cell	3.99e-11	57
myoblast	3.99e-11	57
multi-potent skeletal muscle stem cell	3.99e-11	57
endothelial cell of vascular tree	4.02e-11	24
endothelial cell	1.01e-09	35
electrically responsive cell	3.61e-09	60
electrically active cell	3.61e-09	60
meso-epithelial cell	3.12e-08	44
blood vessel endothelial cell	1.59e-07	18
embryonic blood vessel endothelial progenitor cell	1.59e-07	18

Uber Anatomy

Ontology term	p-value	n
vessel	1.95e-23	69
vasculature	3.78e-23	79
vascular system	3.78e-23	79
blood vessel	1.56e-21	60
epithelial tube open at both ends	1.56e-21	60
blood vasculature	1.56e-21	60
vascular cord	1.56e-21	60
splanchnic layer of lateral plate mesoderm	3.06e-20	84
artery	9.28e-18	42
arterial blood vessel	9.28e-18	42
arterial system	9.28e-18	42
circulatory system	1.26e-17	113
cardiovascular system	1.86e-17	110
anatomical cluster	2.27e-16	286
systemic artery	1.33e-15	33
systemic arterial system	1.33e-15	33
anatomical conduit	9.06e-15	241
tube	4.62e-14	194
cell layer	8.97e-13	312
muscle tissue	1.55e-12	63
musculature	1.55e-12	63
musculature of body	1.55e-12	63
skeletal muscle tissue	1.97e-12	61
striated muscle tissue	1.97e-12	61
myotome	1.97e-12	61
epithelium	3.84e-12	309
epithelial tube	4.67e-12	118
dermomyotome	7.48e-12	70
somite	1.07e-11	83
paraxial mesoderm	1.07e-11	83
presomitic mesoderm	1.07e-11	83
presumptive segmental plate	1.07e-11	83
trunk paraxial mesoderm	1.07e-11	83
presumptive paraxial mesoderm	1.07e-11	83
organism subdivision	1.78e-11	365
aorta	7.82e-11	21
aortic system	7.82e-11	21
unilaminar epithelium	3.26e-10	138
multi-cellular organism	3.36e-10	659
multilaminar epithelium	1.12e-09	82
anatomical system	2.20e-09	625
multi-tissue structure	2.97e-09	347
anatomical group	3.48e-09	626
endothelium	1.59e-07	18
blood vessel endothelium	1.59e-07	18
cardiovascular system endothelium	1.59e-07	18
trunk mesenchyme	2.27e-07	143
squamous epithelium	4.34e-07	25

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

TF	#promoters	Enrichment	p-value	q-value
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0166749941706542
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00435796651034815
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185631785547686
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00627488712880475
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189412268114348
USF2#7392	3	12.9921973850696	0.000455897939342781	0.0042028003254498

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.