Coexpression cluster:C2409

Full id: C2409_embryonic_Mallassezderived_acute_Endothelial_Smooth_mucinous_iPS

Phase1 CAGE Peaks

Hg19::chr17:41150479..41150500,+	p2@RPL27
Hg19::chr18:47018784..47018858,-	p1@RPL17
Hg19::chr3:23958661..23958672,+	p3@RPL15
Hg19::chr5:180670839..180670850,-	p2@GNB2L1

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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p.value	FDR	nGenes	nPathway	Name
1.29278039819306e-07	4.22792693532735e-05	3	92	Ribosome (KEGG):03010
1.33583789425825e-07	4.22792693532735e-05	3	93	Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
4.38101132167368e-06	0.000462196694436573	3	296	Metabolism of proteins (Reactome):REACT_17015
2.47401672121621e-07	5.22017528176621e-05	3	114	Regulation of beta-cell development (Reactome):REACT_13698
1.26014008745975e-05	0.000997085844202525	3	421	Gene Expression (Reactome):REACT_71
5.131046541619e-06	0.000463993208692118	3	312	Diabetes pathways (Reactome):REACT_15380
4.90583318576651e-07	6.21078481318041e-05	3	143	Influenza Infection (Reactome):REACT_6167
4.4062091595204e-07	6.21078481318041e-05	3	138	{RPS27A,138} (Static Module):NA

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:0003735	structural constituent of ribosome	0.00100743510006639
GO:0005840	ribosome	0.00100743510006639
GO:0030529	ribonucleoprotein complex	0.00143724057864277
GO:0006412	translation	0.00143724057864277
GO:0009059	macromolecule biosynthetic process	0.00248269631372499
GO:0044249	cellular biosynthetic process	0.00390412900224879
GO:0009058	biosynthetic process	0.00671554975359331
GO:0005737	cytoplasm	0.00783500691595296
GO:0043232	intracellular non-membrane-bound organelle	0.00783500691595296
GO:0043228	non-membrane-bound organelle	0.00783500691595296
GO:0043025	cell soma	0.0123445740741651
GO:0003723	RNA binding	0.0131171125191485
GO:0032991	macromolecular complex	0.0138540533694944
GO:0044444	cytoplasmic part	0.0209145093649791
GO:0015934	large ribosomal subunit	0.0270742205951243
GO:0010467	gene expression	0.029605707070642
GO:0044267	cellular protein metabolic process	0.029605707070642
GO:0044260	cellular macromolecule metabolic process	0.029605707070642
GO:0019538	protein metabolic process	0.0310029748407682
GO:0044424	intracellular part	0.0349162005738084
GO:0033279	ribosomal subunit	0.0410395691737379

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
animal cell	2.50e-50	679
eukaryotic cell	2.50e-50	679
embryonic cell	2.46e-37	248
native cell	1.35e-31	722
somatic cell	2.96e-26	591
epithelial cell	3.54e-26	254
mesodermal cell	1.04e-22	119
non-terminally differentiated cell	1.15e-20	180
electrically responsive cell	7.43e-16	60
electrically active cell	7.43e-16	60
muscle precursor cell	1.44e-15	57
myoblast	1.44e-15	57
multi-potent skeletal muscle stem cell	1.44e-15	57
contractile cell	4.20e-15	59
muscle cell	8.59e-15	54
smooth muscle cell	9.39e-14	42
smooth muscle myoblast	9.39e-14	42
vascular associated smooth muscle cell	1.88e-12	32
squamous epithelial cell	6.20e-11	62
lining cell	7.34e-08	57
barrier cell	7.34e-08	57
blood vessel endothelial cell	2.72e-07	18
embryonic blood vessel endothelial progenitor cell	2.72e-07	18
ectodermal cell	5.67e-07	71

Uber Anatomy

Ontology term	p-value	n
artery	1.27e-15	42
arterial blood vessel	1.27e-15	42
arterial system	1.27e-15	42
vasculature	1.74e-15	79
vascular system	1.74e-15	79
multilaminar epithelium	4.98e-15	82
unilaminar epithelium	8.44e-15	138
epithelial tube	1.02e-14	118
dermomyotome	1.56e-14	70
blood vessel	2.48e-14	60
epithelial tube open at both ends	2.48e-14	60
blood vasculature	2.48e-14	60
vascular cord	2.48e-14	60
vessel	5.82e-14	69
somite	1.37e-13	83
paraxial mesoderm	1.37e-13	83
presomitic mesoderm	1.37e-13	83
presumptive segmental plate	1.37e-13	83
trunk paraxial mesoderm	1.37e-13	83
presumptive paraxial mesoderm	1.37e-13	83
trunk mesenchyme	6.94e-13	143
splanchnic layer of lateral plate mesoderm	9.32e-13	84
mesenchyme	1.53e-12	238
entire embryonic mesenchyme	1.53e-12	238
skeletal muscle tissue	3.66e-12	61
striated muscle tissue	3.66e-12	61
myotome	3.66e-12	61
trunk	6.22e-12	216
systemic artery	1.88e-11	33
systemic arterial system	1.88e-11	33
muscle tissue	1.21e-10	63
musculature	1.21e-10	63
musculature of body	1.21e-10	63
cardiovascular system	9.64e-10	110
circulatory system	1.46e-08	113
endothelium	2.72e-07	18
blood vessel endothelium	2.72e-07	18
cardiovascular system endothelium	2.72e-07	18
simple squamous epithelium	5.82e-07	22

Disease

Ontology term	p-value	n
disease of cellular proliferation	3.93e-11	239
cancer	1.27e-10	235

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
BCL3#602	3	25.9103271028037	9.48553136097325e-05	0.00137362646950733
BCLAF1#9774	3	16.2394857075914	0.00038025670676648	0.00376611002351677
BRCA1#672	2	10.0921153216119	0.013771396990026	0.0484690614760843
CHD2#1106	3	7.75801712558764	0.00335152246453634	0.0172939552704403
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160829268677346
ELK4#2005	3	12.176761243851	0.000891263257762061	0.0066369086187103
EP300#2033	4	6.7739417262232	0.000474845982144264	0.00433955543657375
ETS1#2113	4	9.72876092220234	0.000111595531741814	0.00154513134556321
FAM48A#55578	1	288.7921875	0.00345823182072735	0.0175762457114674
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378563833217135
GTF2B#2959	4	31.9438299343242	9.59435337635006e-07	4.08489470963157e-05
GTF2F1#2962	4	12.7396608767577	3.79492332235515e-05	0.000717483701780322
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185923731026833
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0320056987202945
JUNB#3726	2	15.3053163299106	0.00612694714847562	0.0270991501816645
JUND#3727	3	5.24599795640327	0.0104343275174842	0.0386834237903707
KAT2A#2648	1	154.0225	0.00647681994931104	0.0281237568055087
MAX#4149	4	6.45255550900712	0.000576761319564549	0.00485268472198517
MEF2C#4208	2	20.655677246312	0.00340257057944504	0.0173558519534389
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00887249298109766
NANOG#79923	2	14.6223892405063	0.00669875771536376	0.0284869724758694
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.007676733611538
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0434871687922876
POU2F2#5452	4	9.10612405774252	0.00014539566517493	0.00188329131529263
REST#5978	4	9.65002871612802	0.000115282561421917	0.00156913794244019
RXRA#6256	2	10.0373085695666	0.0139170380592011	0.0488778806828161
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00795843155283893
SIX5#147912	4	17.086715355459	1.17257016123224e-05	0.000297454590888835
SRF#6722	4	13.7971782621678	2.75840773062708e-05	0.000583996239568135
STAT1#6772	2	10.3532937485996	0.0131077747617126	0.0464906231181995
STAT2#6773	2	32.6318855932203	0.00137958877512552	0.00898328275362142
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321986997479686
TAF7#6879	4	11.4330694049239	5.85061525419808e-05	0.000968509124319533
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244010941196463
TCF12#6938	4	10.6344649021864	7.8163066689251e-05	0.00120012827432501
TCF7L2#6934	3	8.07763242235301	0.00297838168583462	0.0158614657532447
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0482960206478706
WRNIP1#56897	3	82.3649732620321	2.99417904077464e-06	0.000101430121582699
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106782408653612
ZBTB33#10009	2	15.8323625149906	0.00573424893032464	0.0258371467291158
ZNF143#7702	4	13.5008765522279	3.00867915035614e-05	0.000620749588668599
ZZZ3#26009	2	119.706606217617	0.000103963068385957	0.00145235405285728

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.