Coexpression cluster:C3520

Full id: C3520_Mesenchymal_Hepatocyte_mature_liver_acute_Cardiac_Mesothelial

Phase1 CAGE Peaks

Hg19::chr15:80445232..80445254,+	p3@FAH
Hg19::chr15:80445261..80445274,+	p5@FAH
Hg19::chr15:80445320..80445379,+	p1@FAH

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
somatic cell	8.50e-18	591
animal cell	5.01e-13	679
eukaryotic cell	5.01e-13	679
contractile cell	1.33e-10	59
non-terminally differentiated cell	1.37e-10	180
muscle cell	1.25e-09	54
embryonic cell	1.63e-09	248
muscle precursor cell	1.89e-09	57
myoblast	1.89e-09	57
multi-potent skeletal muscle stem cell	1.89e-09	57
mesodermal cell	4.32e-09	119
smooth muscle cell	2.24e-08	42
smooth muscle myoblast	2.24e-08	42
electrically responsive cell	5.82e-08	60
electrically active cell	5.82e-08	60
multi fate stem cell	5.83e-08	430
somatic stem cell	1.08e-07	436
stem cell	2.51e-07	444

Uber Anatomy

Ontology term	p-value	n
trunk mesenchyme	5.11e-16	143
trunk	1.04e-13	216
epithelial tube	7.13e-12	118
mesenchyme	6.62e-11	238
entire embryonic mesenchyme	6.62e-11	238
dermomyotome	2.38e-10	70
somite	2.66e-10	83
paraxial mesoderm	2.66e-10	83
presomitic mesoderm	2.66e-10	83
presumptive segmental plate	2.66e-10	83
trunk paraxial mesoderm	2.66e-10	83
presumptive paraxial mesoderm	2.66e-10	83
multilaminar epithelium	5.03e-10	82
unilaminar epithelium	1.19e-09	138
skeletal muscle tissue	3.68e-09	61
striated muscle tissue	3.68e-09	61
myotome	3.68e-09	61
muscle tissue	1.29e-08	63
musculature	1.29e-08	63
musculature of body	1.29e-08	63
liver	3.16e-08	19
digestive gland	3.16e-08	19
liver bud	3.16e-08	19
abdomen element	5.02e-08	55
abdominal segment element	5.02e-08	55
abdominal segment of trunk	1.04e-07	61
abdomen	1.04e-07	61
trunk region element	1.53e-07	107
subdivision of trunk	2.14e-07	113
epithelial sac	2.28e-07	25
mesoderm	2.85e-07	448
mesoderm-derived structure	2.85e-07	448
presumptive mesoderm	2.85e-07	448
sac	2.91e-07	26
hepatic diverticulum	7.50e-07	22
liver primordium	7.50e-07	22
epithelium of foregut-midgut junction	8.34e-07	25
anatomical boundary	8.34e-07	25
hepatobiliary system	8.34e-07	25
foregut-midgut junction	8.34e-07	25
septum transversum	8.34e-07	25
digestive tract diverticulum	9.71e-07	23

Disease

Ontology term	p-value	n
myeloid leukemia	8.34e-13	31
leukemia	2.43e-11	39
hematologic cancer	1.26e-09	51
immune system cancer	1.26e-09	51

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
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319928351551403
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127854202571431
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156489525342666
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276070307475196
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246037081217192
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139903772248733
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.010919413526017

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.