Coexpression cluster:C1278

Full id: C1278_Smooth_Endothelial_osteosarcoma_schwannoma_large_Renal_Lymphatic

Phase1 CAGE Peaks

Hg19::chr5:54274654..54274657,-	p@chr5:54274654..54274657 -
Hg19::chr5:54274696..54274727,-	p@chr5:54274696..54274727 -
Hg19::chr5:54275165..54275184,-	p@chr5:54275165..54275184 -
Hg19::chr5:54281153..54281165,-	p1@AB590689
Hg19::chr5:54281407..54281429,-	p1@ESM1
Hg19::chr5:54281512..54281517,-	p4@ESM1
Hg19::chr5:54281535..54281547,-	p2@ESM1

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:0005520	insulin-like growth factor binding	0.0192020879940343
GO:0019838	growth factor binding	0.0192020879940343
GO:0001558	regulation of cell growth	0.0192020879940343
GO:0016049	cell growth	0.0192020879940343
GO:0040008	regulation of growth	0.0192020879940343
GO:0008361	regulation of cell size	0.0192020879940343
GO:0008083	growth factor activity	0.0202141259188239
GO:0000902	cell morphogenesis	0.0297042008451404
GO:0032989	cellular structure morphogenesis	0.0297042008451404
GO:0065008	regulation of biological quality	0.0487975391498881
GO:0005102	receptor binding	0.0487975391498881
GO:0009653	anatomical structure morphogenesis	0.0487975391498881

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	2.01e-35	121
endothelial cell of vascular tree	7.36e-31	24
endothelial cell	1.90e-30	36
meso-epithelial cell	1.07e-24	45
lining cell	1.06e-20	58
barrier cell	1.06e-20	58
blood vessel endothelial cell	1.09e-20	18
embryonic blood vessel endothelial progenitor cell	1.09e-20	18
vascular associated smooth muscle cell	2.18e-19	32
muscle precursor cell	1.64e-16	58
myoblast	1.64e-16	58
multi-potent skeletal muscle stem cell	1.64e-16	58
smooth muscle cell	1.42e-14	43
smooth muscle myoblast	1.42e-14	43
muscle cell	1.31e-13	55
embryonic cell	3.36e-13	250
aortic smooth muscle cell	2.94e-12	10
contractile cell	2.99e-12	59
lymphangioblast	4.34e-12	6
endothelial cell of lymphatic vessel	4.34e-12	6
vascular lymphangioblast	4.34e-12	6
electrically responsive cell	1.22e-11	61
electrically active cell	1.22e-11	61
smooth muscle cell of the subclavian artery	1.30e-11	5
endothelial cell of artery	1.61e-11	9
non-terminally differentiated cell	6.99e-09	106
fenestrated cell	4.32e-07	5
glomerular endothelial cell	4.32e-07	5
capillary endothelial cell	5.74e-07	3
endothelial cell of umbilical vein	6.23e-07	3

Uber Anatomy

Ontology term	p-value	n
vessel	2.91e-46	68
epithelial tube open at both ends	1.69e-39	59
blood vessel	1.69e-39	59
blood vasculature	1.69e-39	59
vascular cord	1.69e-39	59
vasculature	1.43e-38	78
vascular system	1.43e-38	78
artery	3.22e-35	42
arterial blood vessel	3.22e-35	42
arterial system	3.22e-35	42
splanchnic layer of lateral plate mesoderm	1.78e-34	83
cardiovascular system	2.90e-32	109
systemic artery	3.66e-31	33
systemic arterial system	3.66e-31	33
circulatory system	5.28e-31	112
epithelial tube	7.81e-29	117
blood vessel endothelium	1.09e-20	18
endothelium	1.09e-20	18
cardiovascular system endothelium	1.09e-20	18
simple squamous epithelium	1.71e-18	22
unilaminar epithelium	1.98e-18	148
squamous epithelium	7.21e-18	25
aorta	3.32e-16	21
aortic system	3.32e-16	21
anatomical conduit	9.36e-16	240
tube	3.39e-15	192
epithelial vesicle	3.81e-15	78
skeletal muscle tissue	5.79e-15	62
striated muscle tissue	5.79e-15	62
myotome	5.79e-15	62
muscle tissue	2.89e-14	64
musculature	2.89e-14	64
musculature of body	2.89e-14	64
blood vessel smooth muscle	2.94e-12	10
arterial system smooth muscle	2.94e-12	10
artery smooth muscle tissue	2.94e-12	10
aorta smooth muscle tissue	2.94e-12	10
somite	3.80e-12	71
presomitic mesoderm	3.80e-12	71
presumptive segmental plate	3.80e-12	71
dermomyotome	3.80e-12	71
trunk paraxial mesoderm	3.80e-12	71
mesoderm	3.98e-12	315
mesoderm-derived structure	3.98e-12	315
presumptive mesoderm	3.98e-12	315
paraxial mesoderm	7.03e-12	72
presumptive paraxial mesoderm	7.03e-12	72
dense mesenchyme tissue	1.28e-11	73
thoracic segment blood vessel	1.30e-11	5
subclavian artery	1.30e-11	5
endothelial tube	1.61e-11	9
arterial system endothelium	1.61e-11	9
endothelium of artery	1.61e-11	9
cell layer	2.31e-11	309
trunk blood vessel	2.98e-11	7
epithelium	4.64e-11	306
multilaminar epithelium	2.78e-10	83
lateral plate mesoderm	3.17e-10	203
trunk mesenchyme	1.45e-09	122
lymphatic vessel	7.63e-09	8
lymph vasculature	7.63e-09	8
lymphatic part of lymphoid system	7.63e-09	8
anatomical cluster	2.64e-08	373
trunk	5.89e-08	199
smooth muscle tissue	1.25e-07	15
microcirculatory vessel	5.74e-07	3
endothelium of capillary	5.74e-07	3
capillary	5.74e-07	3
lymphoid system	6.70e-07	10

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
GATA2#2624	3	5.46211360009457	0.0132836836259278	0.0469805158892067
JUN#3725	3	5.36264108242986	0.0139726108558902	0.0490565604994896
MAX#4149	4	3.6871745765755	0.0136057064395334	0.048016976137547
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223592353423507
STAT3#6774	4	6.01112285551671	0.00225577915639448	0.0128115351196195

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.