Coexpression cluster:C2341

Full id: C2341_Smooth_Fibroblast_mesenchymal_Hepatic_Adipocyte_Pericytes_Preadipocyte

Phase1 CAGE Peaks

Hg19::chr15:64455164..64455227,-	p1@PPIB
Hg19::chr19:13049413..13049432,+	p1@CALR
Hg19::chr3:127771233..127771316,+	p1@SEC61A1
Hg19::chr3:128369643..128369678,-	p1@RPN1

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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p.value	FDR	nGenes	nPathway	Name
7.83254338792028e-07	0.000495799996455354	3	167	Protein processing in endoplasmic reticulum (KEGG):04141
0.000176767794609482	0.0223788027975604	2	156	Phagosome (KEGG):04145
5.131046541619e-06	0.00162397623042241	3	312	Diabetes pathways (Reactome):REACT_15380
1.44809941098012e-05	0.00229161731787605	3	441	AR up reg. targets (Netpath):NetPath_2
8.74889515724365e-06	0.00184601687817841	2	35	{INS,35} (Static Module):NA

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:0044432	endoplasmic reticulum part	9.33494354018741e-06
GO:0005783	endoplasmic reticulum	4.32238704894574e-05
GO:0005788	endoplasmic reticulum lumen	0.00119892517736691
GO:0048770	pigment granule	0.00121336223236269
GO:0042470	melanosome	0.00121336223236269
GO:0051082	unfolded protein binding	0.00450023955118235
GO:0044446	intracellular organelle part	0.00450023955118235
GO:0044422	organelle part	0.00450023955118235
GO:0040020	regulation of meiosis	0.00450023955118235
GO:0044444	cytoplasmic part	0.00573535899024002
GO:0006457	protein folding	0.00838247864021421
GO:0016023	cytoplasmic membrane-bound vesicle	0.00838247864021421
GO:0031988	membrane-bound vesicle	0.00838247864021421
GO:0031410	cytoplasmic vesicle	0.0109134708244856
GO:0031982	vesicle	0.0109134708244856
GO:0005789	endoplasmic reticulum membrane	0.0112394684514031
GO:0042175	nuclear envelope-endoplasmic reticulum network	0.0112394684514031
GO:0030867	rough endoplasmic reticulum membrane	0.012370741454421
GO:0006886	intracellular protein transport	0.0127422358547018
GO:0030866	cortical actin cytoskeleton organization and biogenesis	0.0127422358547018
GO:0030865	cortical cytoskeleton organization and biogenesis	0.0127422358547018
GO:0006611	protein export from nucleus	0.0127422358547018
GO:0008250	oligosaccharyl transferase complex	0.0127422358547018
GO:0018279	protein amino acid N-linked glycosylation via asparagine	0.0127422358547018
GO:0018196	peptidyl-asparagine modification	0.0127422358547018
GO:0005791	rough endoplasmic reticulum	0.0127422358547018
GO:0004579	dolichyl-diphosphooligosaccharide-protein glycotransferase activity	0.0127422358547018
GO:0004576	oligosaccharyl transferase activity	0.013009355382734
GO:0005737	cytoplasm	0.0139458562098636
GO:0022884	macromolecule transmembrane transporter activity	0.0169667838835292
GO:0015450	P-P-bond-hydrolysis-driven protein transmembrane transporter activity	0.0169667838835292
GO:0008320	protein transmembrane transporter activity	0.0176993602305049
GO:0015031	protein transport	0.0196169772724579
GO:0046907	intracellular transport	0.0202639729663448
GO:0045184	establishment of protein localization	0.0202639729663448
GO:0043231	intracellular membrane-bound organelle	0.0202639729663448
GO:0043227	membrane-bound organelle	0.0202639729663448
GO:0008104	protein localization	0.0202639729663448
GO:0031974	membrane-enclosed lumen	0.0202639729663448
GO:0043233	organelle lumen	0.0202639729663448
GO:0005515	protein binding	0.02060231316098
GO:0033036	macromolecule localization	0.02060231316098
GO:0051168	nuclear export	0.02060231316098
GO:0012505	endomembrane system	0.02060231316098
GO:0009897	external side of plasma membrane	0.0224202744666166
GO:0051649	establishment of cellular localization	0.0224202744666166
GO:0006487	protein amino acid N-linked glycosylation	0.022571110402564
GO:0051641	cellular localization	0.022571110402564
GO:0009306	protein secretion	0.0235002266741561
GO:0051327	M phase of meiotic cell cycle	0.0267922280755042
GO:0065002	intracellular protein transport across a membrane	0.0267922280755042
GO:0007126	meiosis	0.0267922280755042
GO:0051321	meiotic cell cycle	0.0270462586568967
GO:0043229	intracellular organelle	0.0315541271581508
GO:0043226	organelle	0.0315541271581508
GO:0003755	peptidyl-prolyl cis-trans isomerase activity	0.0329087021205927
GO:0016859	cis-trans isomerase activity	0.0329087021205927
GO:0031090	organelle membrane	0.0331285673484481
GO:0006874	cellular calcium ion homeostasis	0.0389554397810922
GO:0055074	calcium ion homeostasis	0.0389554397810922
GO:0018193	peptidyl-amino acid modification	0.0393270725751541
GO:0006875	cellular metal ion homeostasis	0.0393270725751541
GO:0055065	metal ion homeostasis	0.0393270725751541
GO:0044267	cellular protein metabolic process	0.0418384575583755
GO:0044260	cellular macromolecule metabolic process	0.0427315939816818
GO:0009986	cell surface	0.0448250058407225
GO:0019538	protein metabolic process	0.0448250058407225
GO:0006913	nucleocytoplasmic transport	0.0448250058407225
GO:0008565	protein transporter activity	0.0448250058407225
GO:0051169	nuclear transport	0.0448250058407225
GO:0006486	protein amino acid glycosylation	0.0483741220471638
GO:0043413	biopolymer glycosylation	0.0483741220471638
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0483741220471638
GO:0044424	intracellular part	0.0483741220471638
GO:0009101	glycoprotein biosynthetic process	0.0483741220471638
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0483741220471638

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	1.78e-44	679
eukaryotic cell	1.78e-44	679
somatic cell	1.60e-39	588
native cell	1.11e-25	722
mesodermal cell	7.96e-24	121
embryonic cell	5.14e-22	250
contractile cell	1.14e-19	59
fibroblast	1.81e-18	76
muscle precursor cell	4.20e-18	58
myoblast	4.20e-18	58
multi-potent skeletal muscle stem cell	4.20e-18	58
muscle cell	1.71e-17	55
smooth muscle cell	4.82e-17	43
smooth muscle myoblast	4.82e-17	43
multi fate stem cell	2.75e-15	427
somatic stem cell	4.40e-15	433
vascular associated smooth muscle cell	2.15e-14	32
non-terminally differentiated cell	2.63e-14	106
electrically responsive cell	1.08e-13	61
electrically active cell	1.08e-13	61
stem cell	1.49e-13	441
epithelial cell	4.83e-07	253
skin fibroblast	6.21e-07	23
lining cell	9.38e-07	58
barrier cell	9.38e-07	58

Uber Anatomy

Ontology term	p-value	n
epithelial tube	1.37e-21	117
unilaminar epithelium	1.48e-19	148
trunk mesenchyme	2.06e-19	122
epithelial vesicle	2.51e-19	78
mesenchyme	6.74e-19	160
entire embryonic mesenchyme	6.74e-19	160
multilaminar epithelium	3.17e-17	83
vasculature	6.26e-17	78
vascular system	6.26e-17	78
trunk	1.00e-16	199
somite	1.58e-16	71
presomitic mesoderm	1.58e-16	71
presumptive segmental plate	1.58e-16	71
dermomyotome	1.58e-16	71
trunk paraxial mesoderm	1.58e-16	71
artery	2.71e-16	42
arterial blood vessel	2.71e-16	42
arterial system	2.71e-16	42
dense mesenchyme tissue	6.19e-16	73
paraxial mesoderm	1.24e-15	72
presumptive paraxial mesoderm	1.24e-15	72
vessel	2.97e-15	68
skeletal muscle tissue	1.06e-14	62
striated muscle tissue	1.06e-14	62
myotome	1.06e-14	62
splanchnic layer of lateral plate mesoderm	1.18e-14	83
epithelial tube open at both ends	2.10e-14	59
blood vessel	2.10e-14	59
blood vasculature	2.10e-14	59
vascular cord	2.10e-14	59
organism subdivision	2.37e-14	264
systemic artery	2.16e-13	33
systemic arterial system	2.16e-13	33
muscle tissue	2.68e-13	64
musculature	2.68e-13	64
musculature of body	2.68e-13	64
cardiovascular system	1.51e-11	109
circulatory system	1.06e-10	112
mesoderm	1.37e-09	315
mesoderm-derived structure	1.37e-09	315
presumptive mesoderm	1.37e-09	315
subdivision of trunk	1.01e-07	112
integument	1.41e-07	46
integumental system	1.41e-07	46
surface structure	3.54e-07	99
aorta	4.39e-07	21
aortic system	4.39e-07	21
abdominal segment of trunk	6.01e-07	60
abdomen	6.01e-07	60

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	2	11.2315872630044	0.0111955903992222	0.0411261041013107
BRCA1#672	2	10.0921153216119	0.013771396990026	0.0484674281462957
CCNT2#905	3	4.75215118272197	0.0138620699668949	0.048712675816707
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106396721019032
E2F4#1874	4	12.6680603152844	3.88145892637771e-05	0.000725959328101651
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160756016480074
ETS1#2113	4	9.72876092220234	0.000111595531741814	0.00154390326395328
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378496094636235
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185800345919022
HMGN3#9324	3	6.13391079251294	0.00664069668332472	0.0282895954033998
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0320020651499573
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0466095485172449
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.018630580745698
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00767366312279263
NFYA#4800	3	13.8191855248729	0.000613241180673451	0.00508626871572066
NFYB#4801	3	12.5698449401523	0.00081145639769735	0.0061864146812989
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0434841423347197
POU2F2#5452	4	9.10612405774252	0.00014539566517493	0.00188259085980715
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00795324352705481
SIX5#147912	3	12.8150365165942	0.000766447113693038	0.0060144992190989
SP2#6668	2	13.0767652469223	0.00833003653661494	0.0328047015779611
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321776337883121
TAF7#6879	3	8.57480205369294	0.0025005543351524	0.0140292986413635
TBP#6908	4	3.70677068709639	0.00529637781478435	0.024384958675642
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0482927615871615
ZNF143#7702	3	10.1256574141709	0.00153486161068818	0.00976304353241143

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.