Coexpression cluster:C2157

Full id: C2157_Mallassezderived_Smooth_Alveolar_Bronchial_Keratocytes_Tracheal_mesothelioma

Phase1 CAGE Peaks

Hg19::chr11:6704513..6704578,-	p1@MRPL17
Hg19::chr12:120720030..120720046,+	p1@NME2P1
Hg19::chr16:67880820..67880844,+	p1@NUTF2
Hg19::chr17:49243792..49243828,+	p2@NME1-NME2 p2@NME2

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:0031967	organelle envelope	0.0286527553894789
GO:0031975	envelope	0.0286527553894789
GO:0006228	UTP biosynthetic process	0.0286527553894789
GO:0046051	UTP metabolic process	0.0286527553894789
GO:0004550	nucleoside diphosphate kinase activity	0.0286527553894789
GO:0046036	CTP metabolic process	0.0286527553894789
GO:0009209	pyrimidine ribonucleoside triphosphate biosynthetic process	0.0286527553894789
GO:0009208	pyrimidine ribonucleoside triphosphate metabolic process	0.0286527553894789
GO:0006241	CTP biosynthetic process	0.0286527553894789
GO:0006183	GTP biosynthetic process	0.0286527553894789
GO:0046039	GTP metabolic process	0.0286527553894789
GO:0009220	pyrimidine ribonucleotide biosynthetic process	0.0286527553894789
GO:0009218	pyrimidine ribonucleotide metabolic process	0.0286527553894789
GO:0009147	pyrimidine nucleoside triphosphate metabolic process	0.032089061554363
GO:0006221	pyrimidine nucleotide biosynthetic process	0.032089061554363
GO:0031090	organelle membrane	0.0353004691211007
GO:0006220	pyrimidine nucleotide metabolic process	0.0353004691211007
GO:0016776	phosphotransferase activity, phosphate group as acceptor	0.0353004691211007
GO:0005643	nuclear pore	0.0393385481596267
GO:0019205	nucleobase, nucleoside, nucleotide kinase activity	0.0393385481596267
GO:0046930	pore complex	0.0393385481596267
GO:0044249	cellular biosynthetic process	0.0393385481596267
GO:0044453	nuclear membrane part	0.0393385481596267
GO:0009206	purine ribonucleoside triphosphate biosynthetic process	0.0393385481596267
GO:0009145	purine nucleoside triphosphate biosynthetic process	0.0393385481596267
GO:0009201	ribonucleoside triphosphate biosynthetic process	0.0393385481596267
GO:0009142	nucleoside triphosphate biosynthetic process	0.0393385481596267
GO:0009205	purine ribonucleoside triphosphate metabolic process	0.0393385481596267
GO:0009144	purine nucleoside triphosphate metabolic process	0.0393385481596267
GO:0009199	ribonucleoside triphosphate metabolic process	0.0393385481596267
GO:0009152	purine ribonucleotide biosynthetic process	0.0393385481596267
GO:0009141	nucleoside triphosphate metabolic process	0.0393385481596267
GO:0031965	nuclear membrane	0.0393385481596267
GO:0009150	purine ribonucleotide metabolic process	0.0393385481596267
GO:0009260	ribonucleotide biosynthetic process	0.0393385481596267
GO:0006164	purine nucleotide biosynthetic process	0.0393385481596267
GO:0006163	purine nucleotide metabolic process	0.0393385481596267
GO:0009259	ribonucleotide metabolic process	0.0393385481596267
GO:0009058	biosynthetic process	0.0393385481596267
GO:0005635	nuclear envelope	0.0438641156314734

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
embryonic cell	7.92e-39	250
animal cell	9.47e-31	679
eukaryotic cell	9.47e-31	679
mesodermal cell	1.83e-29	121
epithelial cell	2.84e-26	253
contractile cell	1.30e-19	59
electrically responsive cell	4.34e-19	61
electrically active cell	4.34e-19	61
muscle precursor cell	9.80e-19	58
myoblast	9.80e-19	58
multi-potent skeletal muscle stem cell	9.80e-19	58
non-terminally differentiated cell	1.80e-18	106
muscle cell	2.90e-18	55
native cell	2.79e-16	722
smooth muscle cell	9.74e-16	43
smooth muscle myoblast	9.74e-16	43
somatic cell	4.91e-14	588
vascular associated smooth muscle cell	9.59e-14	32
lining cell	2.23e-10	58
barrier cell	2.23e-10	58
squamous epithelial cell	1.85e-09	63
meso-epithelial cell	5.25e-09	45
endothelial cell	1.38e-08	36
epithelial cell of nephron	3.19e-08	15
ectodermal cell	1.39e-07	72
kidney cortical cell	3.52e-07	12
renal cortical epithelial cell	3.52e-07	12
blood vessel endothelial cell	3.97e-07	18
embryonic blood vessel endothelial progenitor cell	3.97e-07	18
endothelial cell of vascular tree	6.24e-07	24

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	1.30e-23	78
unilaminar epithelium	2.31e-22	148
multilaminar epithelium	7.90e-21	83
somite	6.67e-20	71
presomitic mesoderm	6.67e-20	71
presumptive segmental plate	6.67e-20	71
dermomyotome	6.67e-20	71
trunk paraxial mesoderm	6.67e-20	71
vasculature	1.05e-19	78
vascular system	1.05e-19	78
dense mesenchyme tissue	2.43e-19	73
paraxial mesoderm	3.78e-19	72
presumptive paraxial mesoderm	3.78e-19	72
mesenchyme	4.08e-19	160
entire embryonic mesenchyme	4.08e-19	160
epithelial tube	5.74e-19	117
trunk	1.36e-18	199
organism subdivision	6.47e-18	264
trunk mesenchyme	3.93e-17	122
skeletal muscle tissue	6.52e-17	62
striated muscle tissue	6.52e-17	62
myotome	6.52e-17	62
splanchnic layer of lateral plate mesoderm	6.79e-17	83
vessel	1.29e-16	68
epithelial tube open at both ends	3.40e-16	59
blood vessel	3.40e-16	59
blood vasculature	3.40e-16	59
vascular cord	3.40e-16	59
muscle tissue	1.55e-15	64
musculature	1.55e-15	64
musculature of body	1.55e-15	64
artery	1.42e-14	42
arterial blood vessel	1.42e-14	42
arterial system	1.42e-14	42
cell layer	4.77e-13	309
cardiovascular system	2.05e-12	109
epithelium	2.47e-12	306
circulatory system	1.33e-11	112
systemic artery	3.10e-10	33
systemic arterial system	3.10e-10	33
multi-tissue structure	2.61e-09	342
nephron epithelium	3.19e-08	15
renal tubule	3.19e-08	15
nephron tubule	3.19e-08	15
nephron	3.19e-08	15
uriniferous tubule	3.19e-08	15
nephrogenic mesenchyme	3.19e-08	15
parenchyma	7.29e-08	15
anatomical cluster	1.22e-07	373
excretory tube	3.42e-07	16
kidney epithelium	3.42e-07	16
cortex of kidney	3.52e-07	12
renal parenchyma	3.52e-07	12
blood vessel endothelium	3.97e-07	18
endothelium	3.97e-07	18
cardiovascular system endothelium	3.97e-07	18
simple squamous epithelium	4.35e-07	22
urinary system structure	7.48e-07	47
larynx	8.48e-07	9

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	4.75215118272197	0.0138620699668949	0.0487044819267463
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378414840331329
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0319887491143752
JUND#3727	3	5.24599795640327	0.0104343275174842	0.0386710692547386
NR2C2#7182	2	16.3073054526204	0.00541182534464822	0.0245506744492101
RXRA#6256	2	10.0373085695666	0.0139170380592011	0.048871306878212

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.