Coexpression cluster:C3722

Full id: C3722_Preadipocyte_mature_Adipocyte_Fibroblast_Hepatic_Smooth_Pericytes

Phase1 CAGE Peaks

Hg19::chr18:46065483..46065540,+	p2@CTIF
Hg19::chr18:46065541..46065568,+	p3@CTIF
Hg19::chr18:46065570..46065579,+	p6@CTIF

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><br>

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Cell Type

Ontology term	p-value	n
fibroblast	1.54e-18	76
mesodermal cell	6.06e-16	121
embryonic cell	1.18e-14	250
contractile cell	1.54e-12	59
muscle cell	4.35e-11	55
muscle precursor cell	4.35e-11	58
myoblast	4.35e-11	58
multi-potent skeletal muscle stem cell	4.35e-11	58
smooth muscle cell	4.98e-11	43
smooth muscle myoblast	4.98e-11	43
electrically responsive cell	7.50e-10	61
electrically active cell	7.50e-10	61
vascular associated smooth muscle cell	2.38e-09	32
fat cell	2.70e-08	15
extraembryonic cell	3.63e-08	19
non-terminally differentiated cell	1.77e-07	106
skin fibroblast	9.49e-07	23

Uber Anatomy

Ontology term	p-value	n
cell layer	4.11e-22	309
epithelium	4.59e-21	306
anatomical cluster	2.81e-20	373
anatomical conduit	2.58e-19	240
multi-cellular organism	6.59e-19	656
tube	4.80e-17	192
multi-tissue structure	8.14e-16	342
splanchnic layer of lateral plate mesoderm	2.01e-15	83
anatomical system	2.64e-15	624
anatomical group	5.71e-15	625
vasculature	7.73e-15	78
vascular system	7.73e-15	78
epithelial tube	7.32e-14	117
trunk mesenchyme	1.77e-12	122
vessel	5.15e-12	68
structure with developmental contribution from neural crest	5.25e-12	132
epithelial vesicle	6.63e-12	78
epithelial tube open at both ends	1.00e-11	59
blood vessel	1.00e-11	59
blood vasculature	1.00e-11	59
vascular cord	1.00e-11	59
multilaminar epithelium	1.97e-11	83
organism subdivision	2.10e-11	264
dense mesenchyme tissue	2.61e-11	73
artery	3.08e-11	42
arterial blood vessel	3.08e-11	42
arterial system	3.08e-11	42
mesenchyme	3.42e-11	160
entire embryonic mesenchyme	3.42e-11	160
unilaminar epithelium	4.69e-11	148
paraxial mesoderm	6.00e-11	72
presumptive paraxial mesoderm	6.00e-11	72
somite	1.22e-10	71
presomitic mesoderm	1.22e-10	71
presumptive segmental plate	1.22e-10	71
dermomyotome	1.22e-10	71
trunk paraxial mesoderm	1.22e-10	71
ectoderm-derived structure	1.27e-10	171
ectoderm	1.27e-10	171
presumptive ectoderm	1.27e-10	171
skeletal muscle tissue	1.36e-10	62
striated muscle tissue	1.36e-10	62
myotome	1.36e-10	62
muscle tissue	1.56e-10	64
musculature	1.56e-10	64
musculature of body	1.56e-10	64
embryonic structure	2.17e-10	564
cardiovascular system	2.38e-10	109
germ layer	3.57e-10	560
germ layer / neural crest	3.57e-10	560
embryonic tissue	3.57e-10	560
presumptive structure	3.57e-10	560
germ layer / neural crest derived structure	3.57e-10	560
epiblast (generic)	3.57e-10	560
systemic artery	6.06e-10	33
systemic arterial system	6.06e-10	33
trunk	6.92e-10	199
circulatory system	8.40e-10	112
developing anatomical structure	1.83e-09	581
embryo	9.74e-09	592
organ part	5.35e-08	218
surface structure	1.83e-07	99
aorta	2.82e-07	21
aortic system	2.82e-07	21
ecto-epithelium	9.83e-07	104

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	0.00129583760015808
BHLHE40#8553	3	44.8718135469774	1.10603738662898e-05	0.000284445798133819
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321982894094702
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461994231260727
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00761816830777024
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127993811877581
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186388376378257
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00719990266211498
MYC#4609	3	5.2222818716094	0.00702084375574015	0.029431239504124
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269466598756819
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276521440551184
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00239585713596197
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246316266138924
SRF#6722	3	13.7971782621678	0.000380661502580019	0.0037491424620855
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00613373634419482
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00615695208597127
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190158125536137
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00421433217268727
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329170426928691
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00388851986373223

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.