Coexpression cluster:C2721

Full id: C2721_Preadipocyte_Smooth_Mast_Fibroblast_Mesenchymal_mesenchymal_Myoblast

Phase1 CAGE Peaks

Hg19::chr3:139108446..139108457,-	p3@COPB2
Hg19::chr3:139108463..139108474,-	p2@COPB2
Hg19::chr3:139108475..139108518,-	p1@COPB2
Hg19::chr6:83902933..83903005,-	p1@PGM3

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:0004610	phosphoacetylglucosamine mutase activity	0.00447427293064877
GO:0006890	retrograde vesicle-mediated transport, Golgi to ER	0.0126741212418515
GO:0030126	COPI vesicle coat	0.0126741212418515
GO:0030663	COPI coated vesicle membrane	0.0126741212418515
GO:0006891	intra-Golgi vesicle-mediated transport	0.0126741212418515
GO:0030137	COPI-coated vesicle	0.0126741212418515
GO:0016868	intramolecular transferase activity, phosphotransferases	0.0185286344708939
GO:0006041	glucosamine metabolic process	0.0195651482442882
GO:0006040	amino sugar metabolic process	0.0203707987891853
GO:0030120	vesicle coat	0.0207290900904621
GO:0030662	coated vesicle membrane	0.0207290900904621
GO:0016866	intramolecular transferase activity	0.0237242956795106
GO:0005798	Golgi-associated vesicle	0.0237242956795106
GO:0048193	Golgi vesicle transport	0.0272703770303969
GO:0030659	cytoplasmic vesicle membrane	0.0272703770303969
GO:0044433	cytoplasmic vesicle part	0.0272703770303969
GO:0012506	vesicle membrane	0.0272703770303969
GO:0030117	membrane coat	0.0272703770303969
GO:0048475	coated membrane	0.0272703770303969
GO:0030135	coated vesicle	0.0327374462988358
GO:0008565	protein transporter activity	0.0327374462988358
GO:0045045	secretory pathway	0.0486385500290966

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	1.13e-26	180
animal cell	3.43e-17	679
eukaryotic cell	3.43e-17	679
fibroblast	6.63e-15	75
muscle precursor cell	1.75e-14	57
myoblast	1.75e-14	57
multi-potent skeletal muscle stem cell	1.75e-14	57
embryonic cell	1.54e-13	248
muscle cell	3.16e-13	54
electrically responsive cell	3.47e-12	60
electrically active cell	3.47e-12	60
vascular associated smooth muscle cell	4.15e-12	32
smooth muscle cell	7.90e-12	42
smooth muscle myoblast	7.90e-12	42
mesodermal cell	1.68e-11	119
contractile cell	1.81e-09	59
native cell	4.11e-09	722
somatic cell	4.84e-09	591
skin fibroblast	5.92e-09	23
preadipocyte	2.80e-07	12
multi fate stem cell	4.76e-07	430
somatic stem cell	6.14e-07	436

Uber Anatomy

Ontology term	p-value	n
somite	3.75e-15	83
paraxial mesoderm	3.75e-15	83
presomitic mesoderm	3.75e-15	83
presumptive segmental plate	3.75e-15	83
trunk paraxial mesoderm	3.75e-15	83
presumptive paraxial mesoderm	3.75e-15	83
dermomyotome	2.42e-12	70
skeletal muscle tissue	1.93e-11	61
striated muscle tissue	1.93e-11	61
myotome	1.93e-11	61
multilaminar epithelium	3.76e-11	82
unilaminar epithelium	4.97e-11	138
artery	7.20e-11	42
arterial blood vessel	7.20e-11	42
arterial system	7.20e-11	42
muscle tissue	7.53e-11	63
musculature	7.53e-11	63
musculature of body	7.53e-11	63
trunk mesenchyme	1.32e-09	143
systemic artery	1.70e-09	33
systemic arterial system	1.70e-09	33
splanchnic layer of lateral plate mesoderm	2.38e-09	84
vasculature	3.47e-09	79
vascular system	3.47e-09	79
surface structure	1.56e-08	95
trunk	5.99e-08	216
blood vessel	6.27e-08	60
epithelial tube open at both ends	6.27e-08	60
blood vasculature	6.27e-08	60
vascular cord	6.27e-08	60
vessel	7.55e-08	69
integument	9.40e-08	45
integumental system	9.40e-08	45
cardiovascular system	4.33e-07	110
skin of body	6.11e-07	40

Disease

Ontology term	p-value	n
ovarian cancer	1.53e-07	14
reproductive organ cancer	6.12e-07	29
female reproductive organ cancer	7.96e-07	27

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
BRCA1#672	3	15.1381729824178	0.000468218442143119	0.00430346439135662
CEBPB#1051	3	5.97836071936861	0.00715383248472697	0.0297368800347224
CHD2#1106	3	7.75801712558764	0.00335152246453634	0.0173050701870624
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0161163819667492
ELK4#2005	3	12.176761243851	0.000891263257762061	0.00663880203818643
ETS1#2113	3	7.29657069165175	0.0040085737751139	0.0192094813480371
FOSL2#2355	3	12.6976504534213	0.00078756857297571	0.00616819454015824
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.00390732224877209
GATA1#2623	3	10.1702311078503	0.00151515816849827	0.00966656102381131
GATA3#2625	3	20.4273872679045	0.000192441557625832	0.00232029598671025
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186418914558532
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.0030794719826188
JUN#3725	3	9.38462189425225	0.00191899450203047	0.0112879677159989
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186394681095036
MYC#4609	4	5.2222818716094	0.00134430939527274	0.0088870951343771
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00768749969981383
NRF1#4899	3	9.15770958578318	0.00206195379173342	0.011964464251061
PBX3#5090	3	16.4358845150581	0.000366943139555461	0.00365923561081188
POU2F2#5452	3	6.82959304330689	0.00486047377520374	0.0227694904731543
RFX5#5993	3	9.03593312039632	0.00214456119132407	0.012386673280649
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00797507881455228
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00685176349008866
SREBF1#6720	3	35.2543870803662	3.78704019553645e-05	0.000725182785078164
STAT3#6774	3	7.88959874786568	0.00319076048168013	0.0167440374809663
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322869800878708
TAF7#6879	4	11.4330694049239	5.85061525419808e-05	0.00097097156607849
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244723444940168
ZBTB33#10009	3	23.7485437724859	0.000122945190881838	0.00165616829491917
ZBTB7A#51341	4	7.3519093078759	0.00034222354001599	0.00347105800677187
ZNF143#7702	3	10.1256574141709	0.00153486161068818	0.00977018417496577

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.