Coexpression cluster:C4683

Full id: C4683_Preadipocyte_giant_Smooth_Fibroblast_melanoma_Ewing_mesenchymal

Phase1 CAGE Peaks

Hg19::chr7:30634439..30634572,+	p1@GARS
Hg19::chr9:95055931..95055951,-	p2@IARS
Hg19::chr9:95055956..95056004,-	p1@IARS

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

---

p.value	FDR	nGenes	nPathway	Name
4.79354634032066e-06	0.00151715741671149	2	63	Aminoacyl-tRNA biosynthesis (KEGG):00970
0.000216998173040322	0.045786614511508	2	421	Gene Expression (Reactome):REACT_71
2.5771754517853e-07	0.00016313520609801	2	15	{EPRS,15} (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

---

GO ID	GO name	FDR corrected p-value
GO:0043038	amino acid activation	0.000174999140341419
GO:0043039	tRNA aminoacylation	0.000174999140341419
GO:0006418	tRNA aminoacylation for protein translation	0.000174999140341419
GO:0016875	ligase activity, forming carbon-oxygen bonds	0.000174999140341419
GO:0016876	ligase activity, forming aminoacyl-tRNA and related compounds	0.000174999140341419
GO:0004812	aminoacyl-tRNA ligase activity	0.000174999140341419
GO:0006399	tRNA metabolic process	0.000386485029551408
GO:0005625	soluble fraction	0.000389759114775116
GO:0006520	amino acid metabolic process	0.00142466075754636
GO:0006519	amino acid and derivative metabolic process	0.0017073527239818
GO:0009308	amine metabolic process	0.0017073527239818
GO:0004820	glycine-tRNA ligase activity	0.0017073527239818
GO:0006426	glycyl-tRNA aminoacylation	0.0017073527239818
GO:0016874	ligase activity	0.0017073527239818
GO:0006807	nitrogen compound metabolic process	0.00175001427911881
GO:0004822	isoleucine-tRNA ligase activity	0.0019143533411074
GO:0006428	isoleucyl-tRNA aminoacylation	0.0019143533411074
GO:0019752	carboxylic acid metabolic process	0.0019143533411074
GO:0006082	organic acid metabolic process	0.0019143533411074
GO:0000267	cell fraction	0.00232389136198941
GO:0006412	translation	0.003964147193353
GO:0009059	macromolecule biosynthetic process	0.00624735990464482
GO:0030141	secretory granule	0.00624735990464482
GO:0045055	regulated secretory pathway	0.00857402855122935
GO:0044249	cellular biosynthetic process	0.00858732448264697
GO:0009058	biosynthetic process	0.0132407701752879
GO:0005524	ATP binding	0.0161792710118105
GO:0032559	adenyl ribonucleotide binding	0.0161792710118105
GO:0030554	adenyl nucleotide binding	0.0169818384858086
GO:0032553	ribonucleotide binding	0.0227218286099275
GO:0032555	purine ribonucleotide binding	0.0227218286099275
GO:0017076	purine nucleotide binding	0.0236857190230647
GO:0045045	secretory pathway	0.0281591605431612
GO:0016070	RNA metabolic process	0.0290317417570611
GO:0000166	nucleotide binding	0.0297015403698842
GO:0032940	secretion by cell	0.0319161544909049
GO:0016023	cytoplasmic membrane-bound vesicle	0.035806545811623
GO:0031988	membrane-bound vesicle	0.035806545811623
GO:0046903	secretion	0.0380420856223659
GO:0031410	cytoplasmic vesicle	0.0404963451850661
GO:0031982	vesicle	0.0404963451850661
GO:0010467	gene expression	0.0404963451850661
GO:0044267	cellular protein metabolic process	0.0414628423752696
GO:0044260	cellular macromolecule metabolic process	0.0415722779567392
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0426561100799306
GO:0019538	protein metabolic process	0.0426561100799306

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>

---

Cell Type

Ontology term	p-value	n
animal cell	5.58e-25	679
eukaryotic cell	5.58e-25	679
fibroblast	2.46e-12	76
native cell	1.02e-11	722
skin fibroblast	1.30e-08	23
somatic cell	3.53e-08	588
non-terminally differentiated cell	3.28e-07	106
embryonic cell	7.08e-07	250

Uber Anatomy

Ontology term	p-value	n
skin of body	2.31e-07	41
integument	3.98e-07	46
integumental system	3.98e-07	46

Disease

Ontology term	p-value	n
disease of cellular proliferation	1.04e-26	239
cancer	1.03e-25	235
cell type cancer	2.09e-15	143
organ system cancer	2.52e-12	137
carcinoma	2.39e-08	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

---

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

---

(#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	0.00130077865582879
BATF#10538	3	24.3578017923036	6.91705216281876e-05	0.00110241112594633
BCL3#602	2	23.0314018691589	0.00246467476084291	0.0138622525363602
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0191118995803189
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115813133666956
CTCFL#140690	2	13.1643162393162	0.00743336703699601	0.0306948212864473
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327680813097614
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.0043896217840429
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.03242682516819
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322441680237666
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464899955220059
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00765157907222642
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00901921924822076
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00244085382497097
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154800855805825
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00389435768289309
GTF2B#2959	2	21.2958866228828	0.00287818058991141	0.0155901821808909
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435923522166111
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.0039353624519036
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109192398851784
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128717655430174
IRF3#3661	2	31.3213014743264	0.00133951467332011	0.0088795666751431
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00446423494502334
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157670029150666
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187412833969845
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00723342727051157
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0296047279152837
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000741195952090615
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270818032253949
NFYA#4800	2	12.2837204665537	0.00851601140372443	0.0324991308873306
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381623297170609
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173659194689079
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00885651543762593
REST#5978	3	9.65002871612802	0.00111263624711459	0.00771239244789279
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278246930609434
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00204034910607808
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247863179887623
SREBF1#6720	2	31.3372329603255	0.0013381626513618	0.0088784936881758
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00376440741103632
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00155346795971563
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00545658661470083
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00617406006517528
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000649086898727583
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.0329431395602874
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191188817171932
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00423268956236294
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331223336380175

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

---

This analysis result is provided for C0 - C305 clusters.