Coexpression cluster:C4590

Full id: C4590_Neutrophils_Eosinophils_Whole_embryonic_osteosarcoma_Fibroblast_CD14

Phase1 CAGE Peaks

Hg19::chr6:30654342..30654353,-	p11@PPP1R18
Hg19::chr6:30654376..30654395,-	p5@PPP1R18
Hg19::chr6:30654401..30654477,-	p1@PPP1R18

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
somatic cell	1.04e-22	591
CD14-positive, CD16-negative classical monocyte	1.14e-15	42
mesodermal cell	2.26e-15	119
classical monocyte	3.34e-13	45
endothelial cell	3.43e-12	35
myeloid leukocyte	3.49e-12	76
native cell	5.03e-12	722
animal cell	7.01e-12	679
eukaryotic cell	7.01e-12	679
somatic stem cell	2.61e-11	436
multi fate stem cell	4.36e-11	430
endothelial cell of vascular tree	8.77e-11	24
meso-epithelial cell	2.52e-10	44
vascular associated smooth muscle cell	4.51e-10	32
stem cell	7.67e-10	444
monopoietic cell	1.14e-09	63
monocyte	1.14e-09	63
monoblast	1.14e-09	63
promonocyte	1.14e-09	63
non-terminally differentiated cell	1.39e-09	180
macrophage dendritic cell progenitor	1.65e-09	65
smooth muscle cell	2.15e-09	42
smooth muscle myoblast	2.15e-09	42
blood vessel endothelial cell	4.13e-09	18
embryonic blood vessel endothelial progenitor cell	4.13e-09	18
granulocyte monocyte progenitor cell	6.18e-09	71
lining cell	6.47e-09	57
barrier cell	6.47e-09	57
myeloid lineage restricted progenitor cell	3.85e-08	70
contractile cell	7.86e-08	59
muscle precursor cell	3.04e-07	57
myoblast	3.04e-07	57
multi-potent skeletal muscle stem cell	3.04e-07	57
muscle cell	5.31e-07	54

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	3.37e-29	216
cardiovascular system	6.09e-23	110
vessel	1.75e-22	69
circulatory system	1.22e-21	113
vasculature	5.80e-21	79
vascular system	5.80e-21	79
blood vessel	4.38e-20	60
epithelial tube open at both ends	4.38e-20	60
blood vasculature	4.38e-20	60
vascular cord	4.38e-20	60
splanchnic layer of lateral plate mesoderm	1.44e-17	84
artery	1.83e-16	42
arterial blood vessel	1.83e-16	42
arterial system	1.83e-16	42
musculoskeletal system	8.10e-14	167
hemolymphoid system	3.59e-13	112
systemic artery	5.29e-13	33
systemic arterial system	5.29e-13	33
mesoderm	7.03e-12	448
mesoderm-derived structure	7.03e-12	448
presumptive mesoderm	7.03e-12	448
hematopoietic system	1.81e-10	102
blood island	1.81e-10	102
epithelial tube	7.08e-10	118
endothelium	4.13e-09	18
blood vessel endothelium	4.13e-09	18
cardiovascular system endothelium	4.13e-09	18
aorta	7.78e-09	21
aortic system	7.78e-09	21
bone marrow	1.44e-08	80
skeletal element	2.87e-08	101
skeletal system	2.87e-08	101
multilaminar epithelium	3.95e-08	82
bone element	4.25e-08	86
simple squamous epithelium	1.60e-07	22
squamous epithelium	3.99e-07	25
somite	5.19e-07	83
paraxial mesoderm	5.19e-07	83
presomitic mesoderm	5.19e-07	83
presumptive segmental plate	5.19e-07	83
trunk paraxial mesoderm	5.19e-07	83
presumptive paraxial mesoderm	5.19e-07	83
dermomyotome	7.82e-07	70
immune system	8.28e-07	115

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190985625952663
CTBP2#1488	3	62.7170003393281	4.049570681927e-06	0.00013045438385249
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00918731365727576
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322231757268761
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00764899861253661
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278094505085945
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203889534825401
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140825918113724
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0110038271474187

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.