Coexpression cluster:C843

Full id: C843_Alveolar_Mesenchymal_Hepatic_Placental_Renal_Smooth_Fibroblast

Phase1 CAGE Peaks

Hg19::chr16:90015139..90015208,+	p1@DEF8
Hg19::chr17:3571863..3571881,-	p1@TAX1BP3
Hg19::chr18:12308232..12308252,+	p1@TUBB6
Hg19::chr19:47354061..47354076,-	p2@AP2S1
Hg19::chr1:113249721..113249731,-	p3@RHOC
Hg19::chr1:113249734..113249762,-	p1@RHOC
Hg19::chr1:113249948..113250035,-	p4@RHOC
Hg19::chr2:242447692..242447726,-	p4@STK25
Hg19::chr2:242447732..242447779,-	p2@STK25
Hg19::chr5:176074455..176074519,+	p1@TSPAN17

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:0030128	clathrin coat of endocytic vesicle	0.0322402009543343
GO:0030669	clathrin-coated endocytic vesicle membrane	0.0322402009543343
GO:0030122	AP-2 adaptor complex	0.0322402009543343
GO:0030666	endocytic vesicle membrane	0.0322402009543343
GO:0003924	GTPase activity	0.0322402009543343
GO:0045334	clathrin-coated endocytic vesicle	0.0322402009543343
GO:0006901	vesicle coating	0.0322402009543343
GO:0048268	clathrin cage assembly	0.0322402009543343
GO:0006900	membrane budding	0.0322402009543343
GO:0005515	protein binding	0.0322402009543343
GO:0030132	clathrin coat of coated pit	0.0418403982307954
GO:0016050	vesicle organization and biogenesis	0.047192048562374
GO:0030178	negative regulation of Wnt receptor signaling pathway	0.048998473354561

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	4.12e-38	250
mesodermal cell	1.14e-36	121
animal cell	1.59e-21	679
eukaryotic cell	1.59e-21	679
somatic cell	2.19e-21	588
contractile cell	8.90e-21	59
muscle precursor cell	1.76e-19	58
myoblast	1.76e-19	58
multi-potent skeletal muscle stem cell	1.76e-19	58
non-terminally differentiated cell	3.86e-19	106
muscle cell	1.03e-18	55
smooth muscle cell	3.16e-17	43
smooth muscle myoblast	3.16e-17	43
electrically responsive cell	7.96e-17	61
electrically active cell	7.96e-17	61
epithelial cell	5.69e-16	253
meso-epithelial cell	2.53e-15	45
lining cell	2.58e-15	58
barrier cell	2.58e-15	58
vascular associated smooth muscle cell	1.12e-14	32
endothelial cell	1.60e-14	36
fibroblast	9.02e-13	76
endothelial cell of vascular tree	2.33e-12	24
blood vessel endothelial cell	7.30e-11	18
embryonic blood vessel endothelial progenitor cell	7.30e-11	18
native cell	2.97e-09	722
squamous epithelial cell	8.52e-09	63
epithelial cell of nephron	1.40e-08	15
kidney cell	1.21e-07	17
kidney epithelial cell	1.21e-07	17
kidney cortical cell	1.65e-07	12
renal cortical epithelial cell	1.65e-07	12

Uber Anatomy

Ontology term	p-value	n
vasculature	2.31e-28	78
vascular system	2.31e-28	78
epithelial tube	4.02e-27	117
splanchnic layer of lateral plate mesoderm	6.65e-26	83
epithelial vesicle	1.12e-24	78
vessel	1.16e-24	68
unilaminar epithelium	3.90e-24	148
epithelial tube open at both ends	3.58e-23	59
blood vessel	3.58e-23	59
blood vasculature	3.58e-23	59
vascular cord	3.58e-23	59
organism subdivision	1.31e-22	264
multilaminar epithelium	3.24e-22	83
mesenchyme	2.79e-21	160
entire embryonic mesenchyme	2.79e-21	160
trunk	6.77e-21	199
somite	1.29e-20	71
presomitic mesoderm	1.29e-20	71
presumptive segmental plate	1.29e-20	71
dermomyotome	1.29e-20	71
trunk paraxial mesoderm	1.29e-20	71
dense mesenchyme tissue	3.09e-20	73
paraxial mesoderm	5.06e-20	72
presumptive paraxial mesoderm	5.06e-20	72
cardiovascular system	1.18e-19	109
circulatory system	1.37e-19	112
trunk mesenchyme	1.72e-19	122
cell layer	2.22e-19	309
epithelium	9.07e-19	306
artery	9.95e-19	42
arterial blood vessel	9.95e-19	42
arterial system	9.95e-19	42
skeletal muscle tissue	1.01e-17	62
striated muscle tissue	1.01e-17	62
myotome	1.01e-17	62
multi-cellular organism	2.33e-17	656
muscle tissue	5.77e-17	64
musculature	5.77e-17	64
musculature of body	5.77e-17	64
anatomical system	1.58e-15	624
anatomical group	2.85e-15	625
systemic artery	1.08e-13	33
systemic arterial system	1.08e-13	33
multi-tissue structure	3.86e-12	342
anatomical cluster	1.12e-11	373
simple squamous epithelium	3.98e-11	22
blood vessel endothelium	7.30e-11	18
endothelium	7.30e-11	18
cardiovascular system endothelium	7.30e-11	18
anatomical conduit	1.02e-10	240
squamous epithelium	1.04e-10	25
mesoderm	1.39e-10	315
mesoderm-derived structure	1.39e-10	315
presumptive mesoderm	1.39e-10	315
developing anatomical structure	1.97e-09	581
embryo	3.05e-09	592
surface structure	5.96e-09	99
compound organ	7.85e-09	68
nephron epithelium	1.40e-08	15
renal tubule	1.40e-08	15
nephron tubule	1.40e-08	15
nephron	1.40e-08	15
uriniferous tubule	1.40e-08	15
nephrogenic mesenchyme	1.40e-08	15
parenchyma	1.88e-08	15
tube	2.60e-08	192
excretory tube	3.17e-08	16
kidney epithelium	3.17e-08	16

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
ATF3#467	3	6.73895235780263	0.00835893577141354	0.0329110643531124
BRF2#55290	1	107.457558139535	0.00926735017471692	0.0350145714817039
CCNT2#905	5	3.16810078848132	0.0122715766979429	0.0444840928380293
CHD2#1106	4	4.13760913364674	0.0113650969219832	0.0416637775083366
CTCF#10664	8	4.28820509846002	4.59406669642002e-05	0.000807335910663656
CTCFL#140690	3	5.92394230769231	0.0119085785576893	0.0433351928915162
E2F1#1869	6	2.94443352892759	0.00701511988615328	0.0296356324646049
E2F6#1876	7	3.51200901218817	0.000845395041948297	0.00637350846647211
EGR1#1958	9	4.48936118532912	4.28342047930016e-06	0.000135562470132615
ELF1#1997	9	3.83228816292678	1.71269377095518e-05	0.000392091242316501
ESR1#2099	4	12.3074413184618	0.000199967480398519	0.00240050617072884
ETS1#2113	6	5.8372565533214	0.000171358751874285	0.0020897403884865
GABPB1#2553	7	4.94737868532752	9.16652307636923e-05	0.00133557826949348
HEY1#23462	9	3.63609993879514	2.70877685450303e-05	0.000578176876982306
IRF1#3659	5	3.81858187678195	0.00546562857545373	0.0247592618864373
PAX5#5079	7	4.66869587182448	0.000134123573520654	0.0017595442651581
POLR2A#5430	10	2.14745317655807	0.000479337749163792	0.004366087143286
RAD21#5885	7	7.24852372681943	7.20863381607108e-06	0.000207686208859765
REST#5978	7	6.75502010128961	1.15734408021362e-05	0.000294593854236973
SIN3A#25942	6	3.24533083608908	0.00422384063048573	0.0201045342998495
SMC3#9126	5	7.52246642246642	0.000245958108351369	0.00267467918347654
STAT1#6772	4	8.28263499887968	0.000902242788343025	0.00662746761652533
TAF1#6872	8	2.67443702859623	0.00155661727806239	0.00988517280211344
TBP#6908	8	2.96541654967711	0.000730287566864471	0.00581729106824487
TCF12#6938	4	4.25378596087457	0.0103111806051884	0.0383016571071728
TFAP2A#7020	5	8.25931718652248	0.000158182952393598	0.00199426235695738
TFAP2C#7022	7	7.56646002690216	5.39952747293911e-06	0.00016488925431178
YY1#7528	10	4.91117074985386	1.22387217331053e-07	7.03080230519133e-06
ZBTB7A#51341	8	5.88152744630072	4.0719212874727e-06	0.000129496768374653
ZNF143#7702	8	10.8007012417823	3.55138054445481e-08	2.36998487336943e-06

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.