Coexpression cluster:C685

Full id: C685_Alveolar_Mesenchymal_Renal_Smooth_Hepatic_Fibroblast_Keratocytes

Phase1 CAGE Peaks

Hg19::chr11:1968548..1968589,+	p1@MRPL23
Hg19::chr11:57508973..57509018,+	p3@C11orf31
Hg19::chr16:1359622..1359697,+	p1@UBE2I
Hg19::chr19:13885252..13885293,+	p1@C19orf53
Hg19::chr19:17970677..17970686,+	p2@RPL18A
Hg19::chr19:18043810..18043835,+	p1@CCDC124
Hg19::chr19:2427539..2427591,-	p1@TIMM13
Hg19::chr19:45582497..45582551,+	p1@GEMIN7
Hg19::chr19:6361517..6361640,+	p1@CLPP
Hg19::chr1:54665832..54665877,+	p1@MRPL37
Hg19::chr3:49059510..49059579,+	p1@NDUFAF3
Hg19::chr7:44163126..44163155,-	p1@POLD2

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:0031974	membrane-enclosed lumen	0.000193512463740142
GO:0043233	organelle lumen	0.000193512463740142
GO:0000313	organellar ribosome	0.00299085559287461
GO:0005761	mitochondrial ribosome	0.00299085559287461
GO:0005739	mitochondrion	0.00299085559287461
GO:0030529	ribonucleoprotein complex	0.00411426777240149
GO:0044446	intracellular organelle part	0.00435327555541477
GO:0044422	organelle part	0.00435327555541477
GO:0043398	HLH domain binding	0.00526904509596138
GO:0015934	large ribosomal subunit	0.00578115676195091
GO:0016604	nuclear body	0.00578115676195091
GO:0044429	mitochondrial part	0.00595076123775477
GO:0043229	intracellular organelle	0.00840756935025863
GO:0043226	organelle	0.00840756935025863
GO:0008462	endopeptidase Clp activity	0.00948204782553061
GO:0003735	structural constituent of ribosome	0.0100779420613185
GO:0031980	mitochondrial lumen	0.0100779420613185
GO:0005759	mitochondrial matrix	0.0100779420613185
GO:0005840	ribosome	0.0109967187094474
GO:0033279	ribosomal subunit	0.0123026770219084
GO:0042719	mitochondrial intermembrane space protein transporter complex	0.0123026770219084
GO:0045039	protein import into mitochondrial inner membrane	0.0123026770219084
GO:0032991	macromolecular complex	0.0123026770219084
GO:0043231	intracellular membrane-bound organelle	0.0123026770219084
GO:0043227	membrane-bound organelle	0.0123026770219084
GO:0007007	inner mitochondrial membrane organization and biogenesis	0.0145791802178139
GO:0000387	spliceosomal snRNP biogenesis	0.0157922524412481
GO:0044424	intracellular part	0.0170194352354491
GO:0006412	translation	0.0197456222733237
GO:0000795	synaptonemal complex	0.0197456222733237
GO:0043681	protein import into mitochondrion	0.0197456222733237
GO:0044444	cytoplasmic part	0.0197456222733237
GO:0000315	organellar large ribosomal subunit	0.0202899870466734
GO:0005762	mitochondrial large ribosomal subunit	0.0202899870466734
GO:0005744	mitochondrial inner membrane presequence translocase complex	0.0202899870466734
GO:0016605	PML body	0.0210389911498501
GO:0043232	intracellular non-membrane-bound organelle	0.0227072814930335
GO:0043228	non-membrane-bound organelle	0.0227072814930335
GO:0005737	cytoplasm	0.0235427243499324
GO:0007006	mitochondrial membrane organization and biogenesis	0.0236577228278529
GO:0006626	protein targeting to mitochondrion	0.0253827994317314
GO:0044451	nucleoplasm part	0.02547497433364
GO:0009059	macromolecule biosynthetic process	0.0276297379577305
GO:0005758	mitochondrial intermembrane space	0.029801120846867
GO:0043170	macromolecule metabolic process	0.029801120846867
GO:0005654	nucleoplasm	0.0303935112857104
GO:0031970	organelle envelope lumen	0.0305183546678942
GO:0000794	condensed nuclear chromosome	0.0305183546678942
GO:0044267	cellular protein metabolic process	0.0307394584809551
GO:0044260	cellular macromolecule metabolic process	0.0318604052842707
GO:0005842	cytosolic large ribosomal subunit (sensu Eukaryota)	0.0356935228895277
GO:0019538	protein metabolic process	0.0356935228895277
GO:0044249	cellular biosynthetic process	0.0405523371864651
GO:0006839	mitochondrial transport	0.0413585107437134
GO:0003887	DNA-directed DNA polymerase activity	0.0413585107437134
GO:0005622	intracellular	0.0413585107437134
GO:0008430	selenium binding	0.0413585107437134
GO:0031981	nuclear lumen	0.0415450125925671
GO:0000793	condensed chromosome	0.0415450125925671
GO:0007059	chromosome segregation	0.0463138328989554
GO:0044237	cellular metabolic process	0.0482158782953958
GO:0044454	nuclear chromosome part	0.0498887043556976
GO:0065002	intracellular protein transport across a membrane	0.0498887043556976
GO:0000398	nuclear mRNA splicing, via spliceosome	0.0498887043556976
GO:0000375	RNA splicing, via transesterification reactions	0.0498887043556976
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0498887043556976

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
animal cell	7.69e-29	679
eukaryotic cell	7.69e-29	679
embryonic cell	4.86e-27	250
mesodermal cell	1.23e-22	121
somatic cell	1.15e-17	588
contractile cell	1.78e-17	59
non-terminally differentiated cell	3.14e-17	106
native cell	9.66e-17	722
muscle cell	3.73e-15	55
electrically responsive cell	4.54e-15	61
electrically active cell	4.54e-15	61
muscle precursor cell	8.22e-15	58
myoblast	8.22e-15	58
multi-potent skeletal muscle stem cell	8.22e-15	58
epithelial cell	2.61e-14	253
smooth muscle cell	6.60e-13	43
smooth muscle myoblast	6.60e-13	43
vascular associated smooth muscle cell	3.07e-10	32
meso-epithelial cell	2.07e-08	45
epithelial cell of nephron	4.16e-08	15
lining cell	5.37e-08	58
barrier cell	5.37e-08	58
endothelial cell	8.55e-08	36
ectodermal cell	2.59e-07	72
kidney cortical cell	3.37e-07	12
renal cortical epithelial cell	3.37e-07	12
kidney cell	4.13e-07	17
kidney epithelial cell	4.13e-07	17
blood vessel endothelial cell	4.37e-07	18
embryonic blood vessel endothelial progenitor cell	4.37e-07	18

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	1.97e-21	78
somite	8.46e-18	71
presomitic mesoderm	8.46e-18	71
presumptive segmental plate	8.46e-18	71
dermomyotome	8.46e-18	71
trunk paraxial mesoderm	8.46e-18	71
multilaminar epithelium	1.92e-17	83
unilaminar epithelium	4.05e-17	148
paraxial mesoderm	4.32e-17	72
presumptive paraxial mesoderm	4.32e-17	72
dense mesenchyme tissue	5.15e-17	73
mesenchyme	1.69e-14	160
entire embryonic mesenchyme	1.69e-14	160
skeletal muscle tissue	2.50e-14	62
striated muscle tissue	2.50e-14	62
myotome	2.50e-14	62
vasculature	7.72e-14	78
vascular system	7.72e-14	78
epithelial tube	7.98e-14	117
trunk mesenchyme	7.17e-13	122
muscle tissue	7.18e-13	64
musculature	7.18e-13	64
musculature of body	7.18e-13	64
vessel	1.55e-12	68
trunk	1.96e-12	199
splanchnic layer of lateral plate mesoderm	2.73e-12	83
epithelial tube open at both ends	3.92e-12	59
blood vessel	3.92e-12	59
blood vasculature	3.92e-12	59
vascular cord	3.92e-12	59
organism subdivision	2.84e-11	264
artery	4.76e-11	42
arterial blood vessel	4.76e-11	42
arterial system	4.76e-11	42
cell layer	7.03e-09	309
epithelium	2.32e-08	306
circulatory system	2.81e-08	112
cardiovascular system	3.05e-08	109
parenchyma	3.59e-08	15
nephron epithelium	4.16e-08	15
renal tubule	4.16e-08	15
nephron tubule	4.16e-08	15
nephron	4.16e-08	15
uriniferous tubule	4.16e-08	15
nephrogenic mesenchyme	4.16e-08	15
systemic artery	1.36e-07	33
systemic arterial system	1.36e-07	33
cortex of kidney	3.37e-07	12
renal parenchyma	3.37e-07	12
blood vessel endothelium	4.37e-07	18
endothelium	4.37e-07	18
cardiovascular system endothelium	4.37e-07	18
excretory tube	4.55e-07	16
kidney epithelium	4.55e-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
ATF3#467	5	9.35965605250365	0.000106266926151988	0.00148117062596923
BCLAF1#9774	6	10.8263238050609	7.02962092283241e-06	0.000202864487305801
BHLHE40#8553	3	11.2179533867444	0.00209247176715069	0.0121193244725738
BRCA1#672	5	8.41009610134324	0.000176031908775319	0.00214048160677442
CCNT2#905	12	6.33620157696263	2.3835512786724e-10	2.44054619601242e-08
CHD2#1106	8	6.89601522274457	2.63477013316703e-06	9.24018663323811e-05
CTCF#10664	6	2.68012818653751	0.0138537507481115	0.0487277093719736
E2F1#1869	8	3.27159280991955	0.00066387851376683	0.00542695742793472
E2F4#1874	4	4.22268677176148	0.0114651023744674	0.0419405893830824
E2F6#1876	8	3.34477048779826	0.000566924613343246	0.00483378559008533
EGR1#1958	8	3.32545272987342	0.000590880184228549	0.00494597543966061
ELF1#1997	11	3.90325646224024	1.12752972864617e-06	4.63432024124665e-05
ELK4#2005	4	5.41189388615601	0.00476866333190955	0.0224107649606849
ESR1#2099	3	7.69215082403862	0.00605532558288018	0.0268608625785943
ETS1#2113	12	9.72876092220234	1.38661421527458e-12	1.92064458924485e-10
GABPB1#2553	10	5.88973653015181	1.60938692426694e-07	8.91685734660555e-06
GATA1#2623	5	5.65012839325018	0.00111039311334309	0.00771219966512199
GTF2F1#2962	5	5.30819203198235	0.00147356422806945	0.00942711022452345
HEY1#23462	12	4.04011104310571	5.2821272507085e-08	3.35763900144093e-06
HMGN3#9324	8	5.45236514890039	1.56099565068508e-05	0.000365699472323686
IRF1#3659	8	5.09144250237593	2.6084996882713e-05	0.000563219141913099
IRF3#3661	3	11.7454880528724	0.00183538959802164	0.0108628728452784
IRF4#3662	5	9.13104695281005	0.000119452296579471	0.00162124475665541
JUND#3727	7	4.0802206327581	0.000497020645947162	0.0043941707645878
MAX#4149	8	4.30170367267141	9.11628330297238e-05	0.0013293710023445
MEF2A#4205	4	6.24774363654802	0.00283471242741202	0.0153722691316519
MXI1#4601	6	4.98078581437965	0.00055237738783609	0.0047162967632614
MYC#4609	11	4.78709171564195	1.25420998476009e-07	7.18532290720566e-06
NANOG#79923	5	12.1853243670886	3.02153395836246e-05	0.000620948416130297
NFKB1#4790	9	4.11604756814538	2.84752237283376e-05	0.000599944299165595
NRF1#4899	5	5.08761643654621	0.00178414175698768	0.0109460130974585
PAX5#5079	9	5.00217414838337	5.4522949797447e-06	0.000165292376020191
POLR2A#5430	12	2.14745317655807	0.000103929203846201	0.00145246381914805
POU2F2#5452	8	6.07074937182835	6.94099287930325e-06	0.000200528452371107
RDBP#7936	2	25.6064006650042	0.00267532742987202	0.0147476259605407
REST#5978	5	4.02084529838668	0.00505569111168918	0.0235477556086922
RFX5#5993	7	7.02794798253047	1.47424002832586e-05	0.000349768637706326
RXRA#6256	4	6.69153904637776	0.00220495472409808	0.0127038818574546
SIN3A#25942	10	4.50740393901261	2.12990021740309e-06	7.75338615564175e-05
SIX5#147912	8	11.391143570306	5.49078835696466e-08	3.46496945748056e-06
SMARCB1#6598	4	6.08423859371914	0.00312231975637376	0.0164096192147705
SMC3#9126	4	5.01497761497761	0.00626178397702115	0.0276288321409426
SP1#6667	10	4.74865114845075	1.29045571010307e-06	5.15190764172227e-05
SP2#6668	6	13.0767652469223	2.36047960027179e-06	8.379542113283e-05
SRF#6722	6	6.8985891310839	9.12062420494223e-05	0.0013298183321792
TAF1#6872	12	3.34304628574529	5.12776278934579e-07	2.39721762737907e-05
TAF7#6879	8	7.62204626994928	1.22550270089133e-06	4.94552846129788e-05
TBP#6908	12	3.70677068709639	1.48467551517722e-07	8.36343183007517e-06
TCF12#6938	6	5.31723245109321	0.000386542592763444	0.00378245309150392
THAP1#55145	5	13.0704769178547	2.15728753020685e-05	0.000475126428442162
USF1#7391	8	4.24099951813864	0.000101216949978379	0.00142408689731805
USF2#7392	6	6.4960986925348	0.000127663267259117	0.00169760936710911
YY1#7528	12	4.91117074985386	5.07192667060765e-09	4.07780561625552e-07
ZBTB33#10009	3	7.91618125749529	0.00559052109277224	0.025278972698101
ZBTB7A#51341	8	4.90127287191726	3.46590017012669e-05	0.000679893215379154
ZEB1#6935	5	7.0368466739766	0.000404901771733203	0.00389495589371317
ZNF143#7702	12	13.5008765522279	2.71467069397623e-14	4.52903342824574e-12

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.