Coexpression cluster:C2143

Full id: C2143_Mesenchymal_Alveolar_Osteoblast_Renal_Adipocyte_Placental_Fibroblast

Phase1 CAGE Peaks

Hg19::chr11:61560053..61560091,-	p1@C11orf10
Hg19::chr17:7307407..7307424,-	p1@C17orf61 p1@PLSCR3
Hg19::chr19:5903739..5903809,-	p1@FUT5 p1@NDUFA11
Hg19::chr2:113342163..113342210,+	p1@CHCHD5

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:0017060	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity	0.0082879592865696
GO:0046920	alpha(1,3)-fucosyltransferase activity	0.0082879592865696
GO:0019317	fucose catabolic process	0.0082879592865696
GO:0042355	L-fucose catabolic process	0.0082879592865696
GO:0042354	L-fucose metabolic process	0.0082879592865696
GO:0006004	fucose metabolic process	0.00941758099038374
GO:0008417	fucosyltransferase activity	0.00968622692758105
GO:0019320	hexose catabolic process	0.0480923729825549
GO:0046365	monosaccharide catabolic process	0.0480923729825549
GO:0046164	alcohol catabolic process	0.0480923729825549
GO:0006486	protein amino acid glycosylation	0.0480923729825549
GO:0043413	biopolymer glycosylation	0.0480923729825549
GO:0009101	glycoprotein biosynthetic process	0.0480923729825549
GO:0044275	cellular carbohydrate catabolic process	0.0480923729825549
GO:0016052	carbohydrate catabolic process	0.0480923729825549
GO:0009100	glycoprotein metabolic process	0.0488322814096535

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
mesodermal cell	3.77e-17	121
contractile cell	1.26e-16	59
embryonic cell	1.86e-16	250
electrically responsive cell	5.52e-15	61
electrically active cell	5.52e-15	61
muscle cell	2.19e-14	55
muscle precursor cell	1.30e-13	58
myoblast	1.30e-13	58
multi-potent skeletal muscle stem cell	1.30e-13	58
smooth muscle cell	9.45e-13	43
smooth muscle myoblast	9.45e-13	43
non-terminally differentiated cell	1.54e-12	106
vascular associated smooth muscle cell	2.05e-09	32
animal cell	4.64e-09	679
eukaryotic cell	4.64e-09	679
somatic cell	1.26e-07	588
epithelial cell	1.76e-07	253

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	1.13e-19	78
somite	2.19e-16	71
presomitic mesoderm	2.19e-16	71
presumptive segmental plate	2.19e-16	71
dermomyotome	2.19e-16	71
trunk paraxial mesoderm	2.19e-16	71
dense mesenchyme tissue	2.40e-16	73
paraxial mesoderm	6.58e-16	72
presumptive paraxial mesoderm	6.58e-16	72
multilaminar epithelium	1.04e-15	83
skeletal muscle tissue	3.65e-14	62
striated muscle tissue	3.65e-14	62
myotome	3.65e-14	62
mesenchyme	3.92e-14	160
entire embryonic mesenchyme	3.92e-14	160
trunk mesenchyme	1.81e-13	122
muscle tissue	3.42e-13	64
musculature	3.42e-13	64
musculature of body	3.42e-13	64
unilaminar epithelium	6.26e-13	148
epithelial tube	9.47e-11	117
trunk	9.58e-11	199
organism subdivision	1.87e-10	264
vasculature	1.99e-09	78
vascular system	1.99e-09	78
splanchnic layer of lateral plate mesoderm	3.61e-08	83
vessel	5.29e-08	68
artery	1.59e-07	42
arterial blood vessel	1.59e-07	42
arterial system	1.59e-07	42
epithelial tube open at both ends	2.07e-07	59
blood vessel	2.07e-07	59
blood vasculature	2.07e-07	59
vascular cord	2.07e-07	59
cell layer	9.09e-07	309
epithelium	9.19e-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
ATF3#467	2	11.2315872630044	0.0111955903992222	0.0411188727565187
CHD2#1106	3	7.75801712558764	0.00335152246453634	0.0172888301231706
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106258584231636
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160544773357236
ETS1#2113	3	7.29657069165175	0.0040085737751139	0.0191962692695273
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.01855540663467
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186208144290661
NANOG#79923	2	14.6223892405063	0.00669875771536376	0.0284800145342917
NRF1#4899	4	12.2102794477109	4.49717228915276e-05	0.00079190722762911
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0434705284869787
POU2F2#5452	4	9.10612405774252	0.00014539566517493	0.00188072552330994
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00794340488996815
SREBF1#6720	2	23.5029247202441	0.00263845490076824	0.0145805381968006
SRF#6722	3	10.3478836966259	0.00143989377840126	0.0092354643691242
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321257064610582
TAF7#6879	4	11.4330694049239	5.85061525419808e-05	0.00096743572915325
TBP#6908	4	3.70677068709639	0.00529637781478435	0.024349535704462
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0482732164559964
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106611171198385
ZBTB33#10009	2	15.8323625149906	0.00573424893032464	0.025833803124587

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.