Coexpression cluster:C345

Full id: C345_Mesenchymal_Fibroblast_Alveolar_Renal_Pericytes_Hepatic_Smooth

Phase1 CAGE Peaks

Hg19::chr10:90751038..90751131,-	p2@ACTA2
Hg19::chr10:99258760..99258810,+	p2@UBTD1
Hg19::chr11:46722117..46722183,-	p1@ARHGAP1
Hg19::chr11:6624970..6625034,+	p1@ILK
Hg19::chr11:66313492..66313546,-	p1@ZDHHC24
Hg19::chr11:67210930..67210974,-	p1@CORO1B
Hg19::chr12:14927297..14927347,+	p1@H2AFJ
Hg19::chr12:58120044..58120095,+	p1@ENST00000542466
Hg19::chr12:6875684..6875720,+	p2@PTMS
Hg19::chr16:128201..128270,+	p1@MPG
Hg19::chr16:128274..128286,+	p2@MPG
Hg19::chr16:30905269..30905292,-	p3@BCL7C
Hg19::chr16:30907927..30907963,+	p1@CTF1
Hg19::chr16:31483451..31483507,+	p1@TGFB1I1
Hg19::chr17:7297833..7297871,-	p2@PLSCR3
Hg19::chr19:11546443..11546485,+	p1@PRKCSH
Hg19::chr19:36630961..36631044,+	p1@CAPNS1
Hg19::chr19:4124079..4124128,-	p1@MAP2K2
Hg19::chr19:48216669..48216685,+	p1@EHD2
Hg19::chr19:48894762..48894830,-	p1@KDELR1
Hg19::chr19:50143268..50143279,-	p3@RRAS
Hg19::chr19:50143346..50143409,-	p1@RRAS
Hg19::chr19:51014403..51014420,-	p3@JOSD2
Hg19::chr19:572543..572579,+	p2@BSG
Hg19::chr1:153599994..153600045,-	p2@S100A13
Hg19::chr1:46768851..46768867,-	p2@LRRC41
Hg19::chr20:33865891..33865939,-	p1@EDEM2 p1@MT1P3
Hg19::chr22:19165917..19166026,-	p3@SLC25A1
Hg19::chr22:43547533..43547590,+	p1@TSPO
Hg19::chr22:50946114..50946140,-	p1@LMF2
Hg19::chr3:52273098..52273181,-	p1@TWF2
Hg19::chrX:153718988..153719008,-	p2@SLC10A3

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:0008283	cell proliferation	0.0340738507394172
GO:0005515	protein binding	0.0340738507394172
GO:0042127	regulation of cell proliferation	0.0340738507394172
GO:0006839	mitochondrial transport	0.0340738507394172
GO:0016798	hydrolase activity, acting on glycosyl bonds	0.0340738507394172
GO:0006843	mitochondrial citrate transport	0.0340738507394172
GO:0008284	positive regulation of cell proliferation	0.0340738507394172
GO:0005509	calcium ion binding	0.0340738507394172
GO:0015746	citrate transport	0.0340738507394172
GO:0006842	tricarboxylic acid transport	0.0340738507394172
GO:0032374	regulation of cholesterol transport	0.0340738507394172
GO:0015137	citrate transmembrane transporter activity	0.0340738507394172
GO:0005046	KDEL sequence binding	0.0340738507394172
GO:0032371	regulation of sterol transport	0.0340738507394172
GO:0005146	leukemia inhibitory factor receptor binding	0.0340738507394172
GO:0032368	regulation of lipid transport	0.0340738507394172
GO:0017177	alpha-glucosidase II complex	0.0340738507394172
GO:0015142	tricarboxylic acid transmembrane transporter activity	0.0340738507394172
GO:0005886	plasma membrane	0.0404754078722562
GO:0007005	mitochondrion organization and biogenesis	0.0418019066043096
GO:0003905	alkylbase DNA N-glycosylase activity	0.0418019066043096
GO:0006307	DNA dealkylation	0.0418019066043096
GO:0046943	carboxylic acid transmembrane transporter activity	0.0452564800025801
GO:0005342	organic acid transmembrane transporter activity	0.0452564800025801
GO:0016043	cellular component organization and biogenesis	0.0453970416460283
GO:0017121	phospholipid scrambling	0.0453970416460283
GO:0017128	phospholipid scramblase activity	0.0453970416460283

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
non-terminally differentiated cell	3.85e-36	180
mesodermal cell	5.08e-30	119
contractile cell	2.37e-24	59
embryonic cell	4.38e-23	248
muscle precursor cell	5.20e-22	57
myoblast	5.20e-22	57
multi-potent skeletal muscle stem cell	5.20e-22	57
muscle cell	1.39e-21	54
smooth muscle cell	1.26e-19	42
smooth muscle myoblast	1.26e-19	42
electrically responsive cell	6.25e-18	60
electrically active cell	6.25e-18	60
somatic cell	3.82e-16	591
vascular associated smooth muscle cell	4.51e-16	32
fibroblast	5.78e-16	75
animal cell	3.65e-11	679
eukaryotic cell	3.65e-11	679
meso-epithelial cell	3.96e-09	44
lining cell	6.06e-09	57
barrier cell	6.06e-09	57
endothelial cell	1.59e-08	35
epithelial cell of nephron	7.44e-07	16

Uber Anatomy

Ontology term	p-value	n
somite	5.55e-25	83
paraxial mesoderm	5.55e-25	83
presomitic mesoderm	5.55e-25	83
presumptive segmental plate	5.55e-25	83
trunk paraxial mesoderm	5.55e-25	83
presumptive paraxial mesoderm	5.55e-25	83
vasculature	8.70e-25	79
vascular system	8.70e-25	79
multilaminar epithelium	4.55e-24	82
splanchnic layer of lateral plate mesoderm	5.76e-24	84
trunk mesenchyme	8.66e-24	143
dermomyotome	5.07e-23	70
trunk	6.72e-22	216
epithelial tube	8.00e-22	118
vessel	2.34e-21	69
blood vessel	1.43e-20	60
epithelial tube open at both ends	1.43e-20	60
blood vasculature	1.43e-20	60
vascular cord	1.43e-20	60
skeletal muscle tissue	3.36e-20	61
striated muscle tissue	3.36e-20	61
myotome	3.36e-20	61
muscle tissue	1.02e-19	63
musculature	1.02e-19	63
musculature of body	1.02e-19	63
cardiovascular system	1.80e-19	110
circulatory system	2.36e-19	113
artery	5.28e-18	42
arterial blood vessel	5.28e-18	42
arterial system	5.28e-18	42
unilaminar epithelium	6.92e-17	138
mesenchyme	2.19e-16	238
entire embryonic mesenchyme	2.19e-16	238
organism subdivision	2.46e-16	365
multi-cellular organism	3.02e-16	659
cell layer	9.37e-15	312
epithelium	2.55e-14	309
systemic artery	3.35e-14	33
systemic arterial system	3.35e-14	33
mesoderm	7.22e-14	448
mesoderm-derived structure	7.22e-14	448
presumptive mesoderm	7.22e-14	448
multi-tissue structure	1.60e-13	347
anatomical system	2.74e-13	625
anatomical group	4.51e-13	626
anatomical cluster	2.06e-10	286
surface structure	5.61e-10	95
embryonic structure	6.66e-10	605
developing anatomical structure	6.66e-10	605
germ layer	8.29e-10	604
embryonic tissue	8.29e-10	604
presumptive structure	8.29e-10	604
epiblast (generic)	8.29e-10	604
embryo	2.37e-09	612
compound organ	8.43e-09	69
anatomical conduit	2.15e-08	241
aorta	3.29e-08	21
aortic system	3.29e-08	21
integument	3.58e-07	45
integumental system	3.58e-07	45
subdivision of trunk	6.92e-07	113
nephron epithelium	7.44e-07	16
nephron	7.44e-07	16
uriniferous tubule	7.44e-07	16
metanephric mesenchyme	7.44e-07	16
nephrogenic mesenchyme	7.44e-07	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
CCNT2#905	19	3.76211968632156	2.45529810576708e-08	1.71524333691109e-06
CTCF#10664	12	2.01009613990314	0.00969345535031931	0.0364740878848537
E2F1#1869	19	2.9137623463346	1.59993879657804e-06	6.080640756034e-05
E2F4#1874	8	3.16701507882111	0.00282406107044875	0.0154549420528504
E2F6#1876	15	2.35179174923315	0.000539327246134273	0.00465934306055235
EGR1#1958	21	3.27349253096915	2.7582276701744e-08	1.89020039137365e-06
ELF1#1997	20	2.66131122425471	2.85023666346111e-06	9.80810105091318e-05
ETS1#2113	9	2.73621400936941	0.00396486941935373	0.0190297333312447
GABPB1#2553	13	2.87124655844901	0.000222292427874146	0.00247690161898517
GATA1#2623	7	2.96631740645635	0.00771706798654559	0.0317633350455914
GTF2F1#2962	7	2.78680081679074	0.0107285115493494	0.0395983537497349
HEY1#23462	26	3.28259022252339	3.02301702543147e-11	3.50023143147492e-09
HMGN3#9324	17	4.34485347803	2.74478412909867e-08	1.8822226504198e-06
IRF1#3659	16	3.81858187678195	5.50305036801123e-07	2.54870544294778e-05
MAX#4149	13	2.62135067553414	0.000554206044192607	0.00473113659060256
MXI1#4601	13	4.04688847418346	5.73151353453395e-06	0.000172405974087901
MYC#4609	16	2.6111409358047	8.34241073906737e-05	0.00125290916764086
NFKB1#4790	18	3.08703567610903	1.64350787647976e-06	6.2258367468868e-05
NRF1#4899	10	3.81571232740966	0.000161517089058047	0.00201033050460415
PAX5#5079	12	2.50108707419169	0.00152926791584763	0.009736951281059
PBX3#5090	5	3.42414260730377	0.0142151091986469	0.049862691932474
POLR2A#5430	32	2.14745317655807	2.38288969218142e-11	2.82802973365608e-09
POU2F2#5452	9	2.56109739124008	0.0061527131154126	0.0272004404444876
RAD21#5885	8	2.58875847386408	0.00954369206705494	0.0359429395186308
SIN3A#25942	19	3.21152530654649	3.34308292587877e-07	1.66261065569454e-05
SIX5#147912	6	3.20375912914856	0.00974306583753332	0.0366383196992094
SMARCB1#6598	7	3.99278157712818	0.0014774161452567	0.0094511738818121
SMC3#9126	8	3.76123321123321	0.000941568627785929	0.00681519758246133
SP1#6667	16	2.84919068907045	2.75078925299075e-05	0.000584992219085931
TAF1#6872	27	2.82069530359759	2.58522491432065e-10	2.63927961707463e-08
TAF7#6879	9	3.21555077013485	0.00129964335226015	0.00870700186456465
TBP#6908	23	2.66424143135053	1.56369160124714e-07	8.7565891229303e-06
TFAP2A#7020	6	3.09724394494593	0.0114018302163594	0.0417779092013597
TFAP2C#7022	9	3.04009554652319	0.00192758658778046	0.011328937289882
THAP1#55145	6	5.88171461303462	0.000464526574850227	0.00427555221210742
USF1#7391	17	3.37954649101673	1.11830647159922e-06	4.60365824151956e-05
USF2#7392	9	3.65405551455082	0.000517259816409865	0.00448204579490831
XRCC4#7518	1	134.321947674419	0.00741863550004163	0.0306388355341999
YY1#7528	15	2.30211128899399	0.000683996464386499	0.00551671223600753
ZBTB7A#51341	18	4.13544898568019	1.73869450393486e-08	1.25666100551179e-06
ZNF143#7702	10	4.21902392257122	6.97820471448877e-05	0.00110608092605326
ZNF263#10127	11	2.82625806272242	0.000951801501666243	0.00685269523180206

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.