Coexpression cluster:C1081

Full id: C1081_papillotubular_Renal_Mast_giant_meningioma_mucinous_gall

Phase1 CAGE Peaks

Hg19::chr3:98699880..98699906,+	p2@ENST00000473756
Hg19::chr3:98699909..98699935,+	p3@ENST00000473756
Hg19::chr3:98700032..98700043,+	p7@ENST00000473756
Hg19::chr3:98700102..98700111,+	p8@ENST00000473756
Hg19::chr3:98700113..98700136,+	p4@ENST00000473756
Hg19::chr3:98700139..98700150,+	p6@ENST00000473756
Hg19::chr3:98700171..98700194,+	p1@ENST00000473756
Hg19::chr3:98700196..98700204,+	p9@ENST00000473756

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
muscle precursor cell	1.06e-18	58
myoblast	1.06e-18	58
multi-potent skeletal muscle stem cell	1.06e-18	58
contractile cell	2.44e-18	59
muscle cell	7.50e-18	55
smooth muscle cell	8.27e-17	43
smooth muscle myoblast	8.27e-17	43
vascular associated smooth muscle cell	4.15e-16	32
animal cell	1.35e-15	679
eukaryotic cell	1.35e-15	679
electrically responsive cell	8.04e-15	61
electrically active cell	8.04e-15	61
embryonic cell	7.93e-14	250
non-terminally differentiated cell	6.00e-13	106
kidney tubule cell	6.85e-12	10
nephron tubule epithelial cell	6.85e-12	10
somatic cell	9.15e-12	588
mesodermal cell	1.72e-11	121
native cell	3.47e-11	722
kidney cell	7.07e-10	17
kidney epithelial cell	7.07e-10	17
aortic smooth muscle cell	1.46e-09	10
epithelial cell of nephron	2.48e-08	15
epithelial cell	4.30e-07	253

Uber Anatomy

Ontology term	p-value	n
multilaminar epithelium	1.66e-19	83
epithelial vesicle	1.93e-18	78
somite	4.26e-18	71
presomitic mesoderm	4.26e-18	71
presumptive segmental plate	4.26e-18	71
dermomyotome	4.26e-18	71
trunk paraxial mesoderm	4.26e-18	71
paraxial mesoderm	1.24e-17	72
presumptive paraxial mesoderm	1.24e-17	72
dense mesenchyme tissue	3.51e-17	73
skeletal muscle tissue	1.33e-16	62
striated muscle tissue	1.33e-16	62
myotome	1.33e-16	62
muscle tissue	1.16e-15	64
musculature	1.16e-15	64
musculature of body	1.16e-15	64
mesenchyme	3.80e-14	160
entire embryonic mesenchyme	3.80e-14	160
trunk mesenchyme	4.85e-14	122
organism subdivision	1.32e-13	264
cell layer	5.60e-12	309
epithelium	5.76e-12	306
nephron tubule epithelium	6.85e-12	10
unilaminar epithelium	1.86e-11	148
trunk	3.69e-11	199
artery	1.86e-10	42
arterial blood vessel	1.86e-10	42
arterial system	1.86e-10	42
pigment epithelium of eye	8.48e-10	11
epithelial tube	9.93e-10	117
blood vessel smooth muscle	1.46e-09	10
arterial system smooth muscle	1.46e-09	10
artery smooth muscle tissue	1.46e-09	10
aorta smooth muscle tissue	1.46e-09	10
systemic artery	3.00e-09	33
systemic arterial system	3.00e-09	33
smooth muscle tissue	7.76e-09	15
multi-tissue structure	1.58e-08	342
nephron epithelium	2.48e-08	15
renal tubule	2.48e-08	15
nephron tubule	2.48e-08	15
nephron	2.48e-08	15
uriniferous tubule	2.48e-08	15
nephrogenic mesenchyme	2.48e-08	15
female organism	9.65e-08	41
vasculature	1.02e-07	78
vascular system	1.02e-07	78
excretory tube	1.37e-07	16
kidney epithelium	1.37e-07	16
external ectoderm	8.43e-07	8

Disease

Ontology term	p-value	n
female reproductive organ cancer	7.82e-12	27
reproductive organ cancer	1.48e-10	29
ovarian cancer	5.05e-10	14

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
BATF#10538	8	24.3578017923036	8.04188698177306e-12	1.0168119061615e-09
BCL11A#53335	8	28.3694551036071	2.37350757777029e-12	3.22349490136218e-10
EBF1#1879	8	8.906466846569	2.52252859723395e-08	1.75868066866833e-06
EP300#2033	8	6.7739417262232	2.25366016107097e-07	1.19054129267623e-05
FOS#2353	8	8.9979553088944	2.32446530602145e-08	1.63698470732012e-06
GATA2#2624	8	12.744931733554	1.43392692074517e-09	1.28107693477934e-07
JUND#3727	8	6.99466394187103	1.74369580801501e-07	9.5746501836635e-06
MEF2A#4205	8	18.7432309096441	6.54751754202692e-11	7.25149718527836e-09
NFKB1#4790	8	5.48806342419384	1.21437192632393e-06	4.90819619246691e-05
POLR2A#5430	8	2.14745317655807	0.00221072578897191	0.012723795363961
SP1#6667	8	5.6983813781409	8.98832477855329e-07	3.86468362102646e-05
TCF12#6938	8	10.6344649021864	6.10437051371448e-09	4.83346741532848e-07
USF1#7391	8	6.36149927720796	3.72538670743375e-07	1.83180631985722e-05

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.