Coexpression cluster:C3167

Full id: C3167_Alveolar_embryonic_Smooth_Mesenchymal_Pericytes_Hepatic_Endothelial

Phase1 CAGE Peaks

Hg19::chr11:60609519..60609536,+	p3@CCDC86
Hg19::chr11:60609537..60609567,+	p2@CCDC86
Hg19::chr11:60609568..60609594,+	p1@CCDC86

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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No GOStat results

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
embryonic cell	3.54e-27	248
animal cell	4.60e-25	679
eukaryotic cell	4.60e-25	679
epithelial cell	3.53e-24	254
mesodermal cell	4.89e-20	119
non-terminally differentiated cell	4.93e-15	180
native cell	7.15e-14	722
contractile cell	9.01e-14	59
muscle precursor cell	1.15e-11	57
myoblast	1.15e-11	57
multi-potent skeletal muscle stem cell	1.15e-11	57
muscle cell	1.96e-11	54
electrically responsive cell	5.29e-11	60
electrically active cell	5.29e-11	60
somatic cell	2.36e-10	591
squamous epithelial cell	5.49e-10	62
smooth muscle cell	9.77e-10	42
smooth muscle myoblast	9.77e-10	42
lining cell	1.83e-08	57
barrier cell	1.83e-08	57
endothelial cell	2.11e-08	35
vascular associated smooth muscle cell	2.65e-08	32
meso-epithelial cell	2.77e-08	44
blood vessel endothelial cell	3.61e-08	18
embryonic blood vessel endothelial progenitor cell	3.61e-08	18
epithelial cell of nephron	1.40e-07	16
endothelial cell of vascular tree	2.21e-07	24
kidney cortical cell	7.11e-07	13
renal cortical epithelial cell	7.11e-07	13

Uber Anatomy

Ontology term	p-value	n
mesenchyme	1.21e-16	238
entire embryonic mesenchyme	1.21e-16	238
unilaminar epithelium	3.03e-15	138
trunk mesenchyme	3.93e-15	143
trunk	4.78e-14	216
dermomyotome	8.46e-14	70
multilaminar epithelium	9.70e-14	82
vasculature	1.85e-13	79
vascular system	1.85e-13	79
epithelial tube	2.45e-13	118
cell layer	6.83e-13	312
somite	9.61e-13	83
paraxial mesoderm	9.61e-13	83
presomitic mesoderm	9.61e-13	83
presumptive segmental plate	9.61e-13	83
trunk paraxial mesoderm	9.61e-13	83
presumptive paraxial mesoderm	9.61e-13	83
epithelium	5.73e-12	309
vessel	1.44e-11	69
blood vessel	4.49e-11	60
epithelial tube open at both ends	4.49e-11	60
blood vasculature	4.49e-11	60
vascular cord	4.49e-11	60
skeletal muscle tissue	4.78e-11	61
striated muscle tissue	4.78e-11	61
myotome	4.78e-11	61
artery	2.66e-10	42
arterial blood vessel	2.66e-10	42
arterial system	2.66e-10	42
muscle tissue	5.24e-10	63
musculature	5.24e-10	63
musculature of body	5.24e-10	63
splanchnic layer of lateral plate mesoderm	4.83e-09	84
simple squamous epithelium	1.96e-08	22
multi-tissue structure	3.34e-08	347
endothelium	3.61e-08	18
blood vessel endothelium	3.61e-08	18
cardiovascular system endothelium	3.61e-08	18
nephron epithelium	1.40e-07	16
nephron	1.40e-07	16
uriniferous tubule	1.40e-07	16
metanephric mesenchyme	1.40e-07	16
nephrogenic mesenchyme	1.40e-07	16
squamous epithelium	3.06e-07	25
cardiovascular system	5.23e-07	110
cortex of kidney	7.11e-07	13
renal parenchyma	7.11e-07	13
systemic artery	7.62e-07	33
systemic arterial system	7.62e-07	33
cortex	8.84e-07	16

Disease

Ontology term	p-value	n
disease of cellular proliferation	8.34e-15	239
cancer	6.63e-14	235
cell type cancer	5.00e-09	143
carcinoma	1.34e-07	106

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	3	22.4631745260087	8.81932387510763e-05	0.00129274577711209
BHLHE40#8553	3	44.8718135469774	1.10603738662898e-05	0.000283747085782717
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00163934150938553
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189224984090919
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0114954349836798
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00658572322678893
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00435648553817523
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320559958371071
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319188029505781
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.046018674209304
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0166915631235264
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00760080787060776
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00242326010441706
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00579541622526194
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153650966325786
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.0038988187868706
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108349501460261
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127645358725349
IRF4#3662	3	21.9145126867441	9.49854535978121e-05	0.00136098035235312
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156193158836157
MAFF#23764	3	56.3153564899452	5.59409009993116e-06	0.000168758283057975
MAX#4149	3	6.45255550900712	0.00372191383426551	0.018581813611399
MEF2A#4205	3	18.7432309096441	0.000151824390562247	0.00194819849194378
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00718325662032851
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293253039915912
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.026865305415029
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00307943700268006
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00469622558858792
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172366594052835
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00136116709499203
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00879735932306164
REST#5978	3	9.65002871612802	0.00111263624711459	0.00765397292928472
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00483132502830808
SETDB1#9869	3	40.3200261780105	1.52461559299059e-05	0.000358140638588269
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275505581539391
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00239038464364593
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245512641640907
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00373962060652381
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.0062780631381975
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000645124521627376
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189580461463611
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00420502736792553
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328068006714216
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.01396435760625
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.0024200265508404

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.