Coexpression cluster:C534

Full id: C534_Mesenchymal_Alveolar_Renal_Placental_Fibroblast_Smooth_Tracheal

Phase1 CAGE Peaks

Hg19::chr11:65655906..65655980,-	p1@FIBP
Hg19::chr16:1823114..1823165,-	p1@MRPS34
Hg19::chr16:1832923..1833008,+	p1@NUBP2
Hg19::chr16:2034183..2034223,+	p1@GFER
Hg19::chr16:30441293..30441370,-	p1@DCTPP1
Hg19::chr16:420514..420555,-	p1@MRPL28
Hg19::chr16:686295..686374,-	p1@C16orf13
Hg19::chr16:838330..838397,-	p1@RPUSD1
Hg19::chr19:1095330..1095381,-	p1@POLR2E
Hg19::chr19:13068012..13068053,-	p1@GADD45GIP1
Hg19::chr19:38865399..38865435,+	p1@PSMD8
Hg19::chr19:56186557..56186601,+	p1@EPN1
Hg19::chr1:1243966..1244033,+	p1@PUSL1
Hg19::chr1:1310530..1310603,-	p1@AURKAIP1
Hg19::chr1:155179012..155179053,+	p1@MTX1
Hg19::chr1:2343951..2344018,-	p1@PEX10
Hg19::chr22:37415776..37415843,+	p1@MPST

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:0001522	pseudouridine synthesis	0.00526578666000325
GO:0005739	mitochondrion	0.00526578666000325
GO:0009982	pseudouridine synthase activity	0.00608784549519806
GO:0043231	intracellular membrane-bound organelle	0.00608784549519806
GO:0043227	membrane-bound organelle	0.00608784549519806
GO:0009451	RNA modification	0.00608784549519806
GO:0016866	intramolecular transferase activity	0.0100573020919188
GO:0045839	negative regulation of mitosis	0.0100573020919188
GO:0016784	3-mercaptopyruvate sulfurtransferase activity	0.0100573020919188
GO:0019754	one-carbon compound catabolic process	0.0139226257429952
GO:0016972	thiol oxidase activity	0.0139226257429952
GO:0009440	cyanate catabolic process	0.0139226257429952
GO:0009439	cyanate metabolic process	0.0139226257429952
GO:0043229	intracellular organelle	0.015407499101058
GO:0043226	organelle	0.015407499101058
GO:0016670	oxidoreductase activity, acting on sulfur group of donors, oxygen as acceptor	0.0212846537901441
GO:0004792	thiosulfate sulfurtransferase activity	0.0212846537901441
GO:0044444	cytoplasmic part	0.0215336050909609
GO:0044429	mitochondrial part	0.0215336050909609
GO:0044424	intracellular part	0.0215336050909609
GO:0045862	positive regulation of proteolysis	0.0215336050909609
GO:0017134	fibroblast growth factor binding	0.0235884805853947
GO:0016783	sulfurtransferase activity	0.0235884805853947
GO:0031980	mitochondrial lumen	0.0237277706888406
GO:0005759	mitochondrial matrix	0.0237277706888406
GO:0016558	protein import into peroxisome matrix	0.031280760004272
GO:0005838	proteasome regulatory particle (sensu Eukaryota)	0.040138139493848
GO:0005515	protein binding	0.045757987491814
GO:0006625	protein targeting to peroxisome	0.045757987491814
GO:0008543	fibroblast growth factor receptor signaling pathway	0.045757987491814
GO:0043574	peroxisomal transport	0.045757987491814
GO:0030162	regulation of proteolysis	0.045757987491814
GO:0005737	cytoplasm	0.045757987491814
GO:0031974	membrane-enclosed lumen	0.045757987491814
GO:0043233	organelle lumen	0.045757987491814
GO:0005743	mitochondrial inner membrane	0.045757987491814
GO:0016853	isomerase activity	0.045757987491814
GO:0019866	organelle inner membrane	0.0493032392319663

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	1.50e-34	250
animal cell	2.44e-26	679
eukaryotic cell	2.44e-26	679
mesodermal cell	5.71e-25	121
epithelial cell	4.01e-22	253
non-terminally differentiated cell	1.08e-17	106
contractile cell	7.19e-17	59
electrically responsive cell	1.28e-15	61
electrically active cell	1.28e-15	61
muscle cell	9.78e-15	55
somatic cell	1.31e-14	588
muscle precursor cell	2.78e-14	58
myoblast	2.78e-14	58
multi-potent skeletal muscle stem cell	2.78e-14	58
smooth muscle cell	2.02e-13	43
smooth muscle myoblast	2.02e-13	43
native cell	1.63e-12	722
vascular associated smooth muscle cell	2.09e-11	32
lining cell	2.59e-10	58
barrier cell	2.59e-10	58
meso-epithelial cell	1.03e-09	45
endothelial cell	8.84e-09	36
epithelial cell of nephron	1.40e-08	15
kidney cell	3.29e-08	17
kidney epithelial cell	3.29e-08	17
squamous epithelial cell	3.55e-08	63
blood vessel endothelial cell	8.87e-08	18
embryonic blood vessel endothelial progenitor cell	8.87e-08	18
ectodermal cell	1.13e-07	72
kidney cortical cell	1.42e-07	12
renal cortical epithelial cell	1.42e-07	12
endothelial cell of vascular tree	9.04e-07	24

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	7.78e-21	78
unilaminar epithelium	5.67e-19	148
multilaminar epithelium	7.25e-18	83
mesenchyme	1.94e-17	160
entire embryonic mesenchyme	1.94e-17	160
somite	3.19e-17	71
presomitic mesoderm	3.19e-17	71
presumptive segmental plate	3.19e-17	71
dermomyotome	3.19e-17	71
trunk paraxial mesoderm	3.19e-17	71
dense mesenchyme tissue	6.26e-17	73
paraxial mesoderm	1.07e-16	72
presumptive paraxial mesoderm	1.07e-16	72
trunk	1.97e-16	199
epithelial tube	7.24e-16	117
organism subdivision	3.51e-15	264
vasculature	4.09e-15	78
vascular system	4.09e-15	78
trunk mesenchyme	8.43e-15	122
skeletal muscle tissue	3.78e-14	62
striated muscle tissue	3.78e-14	62
myotome	3.78e-14	62
vessel	9.06e-14	68
epithelial tube open at both ends	1.32e-13	59
blood vessel	1.32e-13	59
blood vasculature	1.32e-13	59
vascular cord	1.32e-13	59
muscle tissue	7.42e-13	64
musculature	7.42e-13	64
musculature of body	7.42e-13	64
artery	8.29e-13	42
arterial blood vessel	8.29e-13	42
arterial system	8.29e-13	42
splanchnic layer of lateral plate mesoderm	9.27e-13	83
cell layer	1.25e-12	309
epithelium	3.22e-12	306
multi-tissue structure	5.09e-09	342
systemic artery	1.00e-08	33
systemic arterial system	1.00e-08	33
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
circulatory system	2.96e-08	112
parenchyma	3.14e-08	15
cardiovascular system	4.33e-08	109
anatomical cluster	5.29e-08	373
blood vessel endothelium	8.87e-08	18
endothelium	8.87e-08	18
cardiovascular system endothelium	8.87e-08	18
simple squamous epithelium	1.14e-07	22
cortex of kidney	1.42e-07	12
renal parenchyma	1.42e-07	12
excretory tube	1.49e-07	16
kidney epithelium	1.49e-07	16
squamous epithelium	1.90e-07	25
urinary system structure	2.88e-07	47
subdivision of trunk	3.09e-07	112
cortex	6.43e-07	15
renal system	8.43e-07	48

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	4	5.28545282964912	0.00585762962104294	0.0262943772024458
BCL3#602	3	6.09654755360088	0.0121612476356288	0.0440948667482792
BCLAF1#9774	7	8.91579607475605	5.76542330868176e-06	0.000173176601937134
BRCA1#672	5	5.93653842447758	0.00111680347517435	0.00766043860132232
CCNT2#905	14	5.21804835749864	2.50272071132719e-09	2.11988360397648e-07
CHD2#1106	9	5.47624738276775	8.66603667249791e-06	0.000235083689360782
CTCF#10664	8	2.52247358732942	0.00710763553513563	0.0296297588174682
CTCFL#140690	6	6.96934389140272	0.000128278927175355	0.00170536187312461
E2F1#1869	11	3.17536949198074	9.04802704927931e-05	0.00132033938381959
E2F4#1874	9	6.70662016691529	1.60415012189843e-06	6.09442832233358e-05
E2F6#1876	14	4.13177530845667	5.72092945550856e-08	3.57563226453536e-06
EGR1#1958	14	4.107912195726	6.17965026005095e-08	3.8234389425916e-06
ELF1#1997	16	4.00762160828945	1.13144653180838e-09	1.04020373534802e-07
ELK4#2005	8	7.64032078045554	3.03218555346911e-06	0.000102651029827799
ETS1#2113	13	7.43964070521355	2.27105563122036e-10	2.32992906747567e-08
GABPB1#2553	13	5.40469940413931	1.23195590443172e-08	9.16411985063708e-07
HEY1#23462	16	3.80245745233479	2.58316753849527e-09	2.17742885030595e-07
HMGN3#9324	13	6.25418355315045	2.00190675212248e-09	1.72648339624211e-07
IRF1#3659	14	6.28942897352321	1.99717530377116e-10	2.06517813416392e-08
IRF3#3661	4	11.0545769909387	0.000390627998014029	0.00382135607761214
JUND#3727	8	3.29160656088048	0.00126043618646503	0.00846442225297207
MAX#4149	8	3.036496710121	0.00215601866543559	0.012444591212525
MXI1#4601	9	5.27377321522551	1.18160458251851e-05	0.00029916509331794
MYC#4609	16	4.91508882033826	4.54175528985501e-11	5.1502321467662e-09
NFKB1#4790	10	3.22827260246696	0.000222289571998704	0.0024771340813031
NFYA#4800	5	5.41928844112662	0.00167818674820208	0.0104900733657815
NFYB#4801	5	4.92935095692249	0.00254959463259559	0.0141096393510837
NR2C2#7182	6	11.5110391430262	7.66053794422864e-06	0.000218178053547122
PAX5#5079	14	5.49258337861704	1.25245751600589e-09	1.14140846870977e-07
PBX3#5090	5	6.44544490786592	0.000770512874507435	0.00604141096851967
POLR2A#5430	17	2.14745317655807	2.27473247069268e-06	8.13041699201481e-05
POU2F2#5452	8	4.28523485070236	0.000204941334679976	0.00243198137173526
RFX5#5993	5	3.54350318446915	0.0104239688604285	0.0386862188200241
RXRA#6256	4	4.72343932685489	0.00868395261593973	0.0330013582438006
SIN3A#25942	16	5.09071503700248	2.6091191843489e-11	3.0755507730724e-09
SIX5#147912	11	11.0561099358852	2.44264174845305e-10	2.49615520123961e-08
SMC3#9126	7	6.19497234791352	6.13164858570721e-05	0.00100546906365627
SP1#6667	12	4.02238685515828	2.1835477628908e-06	7.8420751309681e-05
SP2#6668	4	6.15377188090462	0.00340594026154522	0.0173586275119813
SRF#6722	7	5.68119104912792	0.000106357256863099	0.00148163872876152
TAF1#6872	17	3.34304628574529	1.22696034516851e-09	1.1191485719568e-07
TAF7#6879	8	5.38026795525831	4.02734747987804e-05	0.000738563904215948
TBP#6908	14	3.05263468349114	3.08185039759894e-06	0.000103861043457514
THAP1#55145	8	14.7619504013418	1.99399089791794e-08	1.42442144587997e-06
USF1#7391	10	3.74205839835762	6.11289652105867e-05	0.00100286647779272
YY1#7528	16	4.62227835280363	1.19680964744564e-10	1.28726676384733e-08
ZBTB33#10009	4	7.45052353646615	0.00169991806629872	0.0106182860601778
ZBTB7A#51341	13	5.62204829425804	7.55171478530207e-09	5.85084228829498e-07
ZEB1#6935	5	4.9671858875129	0.00246549333212175	0.0138526822742341
ZNF143#7702	9	7.14752288059124	9.38784177277639e-07	4.02321217442344e-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.