Coexpression cluster:C1636

Full id: C1636_Mesenchymal_Alveolar_Placental_Smooth_Fibroblast_Bronchial_Hair

Phase1 CAGE Peaks

Hg19::chr11:507184..507269,-	p1@RNH1
Hg19::chr17:1945301..1945344,+	p1@OVCA2
Hg19::chr19:47354082..47354132,-	p1@AP2S1
Hg19::chr22:50963976..50964055,-	p1@SCO2
Hg19::chr9:130477912..130477961,-	p1@PTRH1

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:0032311	angiogenin-PRI complex	0.0126567374393484
GO:0004045	aminoacyl-tRNA hydrolase activity	0.0126567374393484
GO:0008428	ribonuclease inhibitor activity	0.0126567374393484
GO:0030128	clathrin coat of endocytic vesicle	0.0151827206402137
GO:0030669	clathrin-coated endocytic vesicle membrane	0.0151827206402137
GO:0030122	AP-2 adaptor complex	0.0151827206402137
GO:0030666	endocytic vesicle membrane	0.0151827206402137
GO:0045334	clathrin-coated endocytic vesicle	0.0151827206402137
GO:0006901	vesicle coating	0.0151827206402137
GO:0048268	clathrin cage assembly	0.0151827206402137
GO:0006900	membrane budding	0.0155268682942639
GO:0030132	clathrin coat of coated pit	0.0205538827115248
GO:0016050	vesicle organization and biogenesis	0.023347032623047
GO:0030125	clathrin vesicle coat	0.0272573686613283
GO:0030139	endocytic vesicle	0.0272573686613283
GO:0030665	clathrin coated vesicle membrane	0.0272573686613283
GO:0006402	mRNA catabolic process	0.0323349158877492
GO:0030100	regulation of endocytosis	0.0357932574808114
GO:0045765	regulation of angiogenesis	0.037889819044312
GO:0005905	coated pit	0.0407195667967789
GO:0006401	RNA catabolic process	0.040882474854515
GO:0030120	vesicle coat	0.040882474854515
GO:0030662	coated vesicle membrane	0.040882474854515
GO:0030131	clathrin adaptor complex	0.040882474854515
GO:0030119	AP-type membrane coat adaptor complex	0.040882474854515
GO:0030118	clathrin coat	0.0480117110439507

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
somatic cell	9.77e-36	588
animal cell	3.16e-35	679
eukaryotic cell	3.16e-35	679
mesodermal cell	3.70e-29	121
embryonic cell	1.25e-28	250
native cell	1.26e-20	722
contractile cell	4.71e-19	59
muscle precursor cell	9.45e-18	58
myoblast	9.45e-18	58
multi-potent skeletal muscle stem cell	9.45e-18	58
muscle cell	6.55e-17	55
smooth muscle cell	6.88e-15	43
smooth muscle myoblast	6.88e-15	43
electrically responsive cell	8.21e-15	61
electrically active cell	8.21e-15	61
non-terminally differentiated cell	4.91e-13	106
vascular associated smooth muscle cell	1.78e-12	32
epithelial cell	2.74e-12	253
meso-epithelial cell	1.46e-11	45
endothelial cell	2.79e-11	36
lining cell	6.11e-11	58
barrier cell	6.11e-11	58
fibroblast	1.13e-08	76
somatic stem cell	3.53e-08	433
multi fate stem cell	7.49e-08	427
blood vessel endothelial cell	9.33e-08	18
embryonic blood vessel endothelial progenitor cell	9.33e-08	18
epithelial cell of nephron	1.68e-07	15
endothelial cell of vascular tree	2.16e-07	24
stem cell	5.24e-07	441

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	4.40e-22	78
multilaminar epithelium	3.14e-19	83
somite	1.55e-18	71
presomitic mesoderm	1.55e-18	71
presumptive segmental plate	1.55e-18	71
dermomyotome	1.55e-18	71
trunk paraxial mesoderm	1.55e-18	71
unilaminar epithelium	2.94e-18	148
vasculature	3.17e-18	78
vascular system	3.17e-18	78
dense mesenchyme tissue	3.71e-18	73
paraxial mesoderm	5.02e-18	72
presumptive paraxial mesoderm	5.02e-18	72
splanchnic layer of lateral plate mesoderm	4.20e-17	83
epithelial tube	4.51e-17	117
vessel	1.55e-16	68
epithelial tube open at both ends	6.85e-16	59
blood vessel	6.85e-16	59
blood vasculature	6.85e-16	59
vascular cord	6.85e-16	59
skeletal muscle tissue	2.73e-15	62
striated muscle tissue	2.73e-15	62
myotome	2.73e-15	62
artery	4.51e-15	42
arterial blood vessel	4.51e-15	42
arterial system	4.51e-15	42
mesoderm	1.25e-14	315
mesoderm-derived structure	1.25e-14	315
presumptive mesoderm	1.25e-14	315
mesenchyme	2.71e-14	160
entire embryonic mesenchyme	2.71e-14	160
trunk mesenchyme	6.11e-14	122
muscle tissue	7.61e-14	64
musculature	7.61e-14	64
musculature of body	7.61e-14	64
trunk	7.78e-14	199
organism subdivision	9.42e-14	264
circulatory system	2.28e-13	112
cardiovascular system	4.40e-13	109
systemic artery	6.17e-11	33
systemic arterial system	6.17e-11	33
lateral plate mesoderm	2.52e-08	203
blood vessel endothelium	9.33e-08	18
endothelium	9.33e-08	18
cardiovascular system endothelium	9.33e-08	18
musculoskeletal system	1.28e-07	167
nephron epithelium	1.68e-07	15
renal tubule	1.68e-07	15
nephron tubule	1.68e-07	15
nephron	1.68e-07	15
uriniferous tubule	1.68e-07	15
nephrogenic mesenchyme	1.68e-07	15
parenchyma	2.05e-07	15
multi-cellular organism	3.04e-07	656
simple squamous epithelium	3.22e-07	22
squamous epithelium	4.07e-07	25
anatomical system	4.73e-07	624
anatomical group	5.08e-07	625
cell layer	5.53e-07	309
epithelium	8.40e-07	306

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
BRF2#55290	1	214.91511627907	0.00464439788813553	0.0219254292383034
CHD2#1106	3	6.20641370047011	0.00777455012627559	0.0319457937851869
E2F1#1869	5	4.90738921487932	0.000351281809925646	0.00352188931043722
EGR1#1958	4	3.99054327584811	0.006780098300144	0.0287567692644874
ELF1#1997	4	3.40647836704603	0.0123506610529955	0.0447242013007106
ELK4#2005	3	9.74140899508082	0.0021255865657434	0.0122859115246929
ESR1#2099	3	18.4611619776927	0.00032663345909756	0.00333007339268744
ETS1#2113	3	5.8372565533214	0.00925327904563143	0.0349652017166577
GABPB1#2553	4	5.65414706894574	0.00177669650209667	0.0109041785263251
IRF1#3659	5	7.6371637535639	3.84754333311872e-05	0.000723372777979454
MXI1#4601	3	5.97694297725558	0.00865300488936688	0.0329400830195221
MYC#4609	4	4.17782549728752	0.00569196903682344	0.0256687920133341
PBX3#5090	3	13.1487076120465	0.000886046932280843	0.00660135936370945
POU2F2#5452	3	5.46367443464551	0.0111565009446978	0.0410012598410616
SIN3A#25942	4	4.32710778145211	0.00497705285576288	0.023237445715187
SIX5#147912	3	10.2520292132754	0.00183229106867769	0.0108476076708593
SP1#6667	4	4.55870510251272	0.0040757356578168	0.0194759222349345
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135154366023781
USF1#7391	5	6.36149927720796	9.59569864925045e-05	0.00136721032909832
YY1#7528	4	3.92893659988308	0.00719386626991762	0.0298320507986471
ZNF143#7702	3	8.10052593133674	0.00362487051209098	0.0183268553716546

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.