Coexpression cluster:C3113

Full id: C3113_Smooth_Fibroblast_lymphangiectasia_colon_gall_mesenchymal_Chondrocyte

Phase1 CAGE Peaks

Hg19::chr11:125462725..125462768,+	p1@STT3A
Hg19::chr11:125462771..125462784,+	p2@STT3A
Hg19::chr20:35807714..35807756,+	p1@RPN2

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
2.88643650599953e-06	0.000913557154148851	2	49	N-Glycan biosynthesis (KEGG):00510
3.40211704163772e-05	0.00717846695785558	2	167	Protein processing in endoplasmic reticulum (KEGG):04141
0.000107161409738044	0.0169582930910455	2	296	Metabolism of proteins (Reactome):REACT_17015
0.000238131011744962	0.0301473860869122	2	441	AR up reg. targets (Netpath):NetPath_2
1.46039942267834e-06	0.000913557154148851	2	35	{INS,35} (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:0018196	peptidyl-asparagine modification	2.70453216891284e-06
GO:0008250	oligosaccharyl transferase complex	2.70453216891284e-06
GO:0018279	protein amino acid N-linked glycosylation via asparagine	2.70453216891284e-06
GO:0004579	dolichyl-diphosphooligosaccharide-protein glycotransferase activity	2.70453216891284e-06
GO:0004576	oligosaccharyl transferase activity	2.70453216891284e-06
GO:0006487	protein amino acid N-linked glycosylation	2.02987218342151e-05
GO:0018193	peptidyl-amino acid modification	9.16662163693145e-05
GO:0006486	protein amino acid glycosylation	0.000145576305078965
GO:0043413	biopolymer glycosylation	0.000145576305078965
GO:0009101	glycoprotein biosynthetic process	0.000145576305078965
GO:0009100	glycoprotein metabolic process	0.000172974356899452
GO:0016758	transferase activity, transferring hexosyl groups	0.00028975026014442
GO:0016757	transferase activity, transferring glycosyl groups	0.000641139106386873
GO:0005789	endoplasmic reticulum membrane	0.000641139106386873
GO:0042175	nuclear envelope-endoplasmic reticulum network	0.000641139106386873
GO:0044432	endoplasmic reticulum part	0.00074540353528002
GO:0005783	endoplasmic reticulum	0.00213141778283036
GO:0012505	endomembrane system	0.00259198081383691
GO:0031090	organelle membrane	0.00530674891805402
GO:0009059	macromolecule biosynthetic process	0.00540140149668042
GO:0009058	biosynthetic process	0.0126675766612062
GO:0006464	protein modification process	0.0146815119011832
GO:0043412	biopolymer modification	0.0152200256949047
GO:0043234	protein complex	0.0152991783171678
GO:0016740	transferase activity	0.0188610573477174
GO:0032991	macromolecular complex	0.0256206593985365
GO:0044446	intracellular organelle part	0.026913961854617
GO:0044422	organelle part	0.026913961854617
GO:0044444	cytoplasmic part	0.0321256485265397
GO:0044267	cellular protein metabolic process	0.0455954016299721
GO:0044260	cellular macromolecule metabolic process	0.0455954016299721
GO:0019538	protein metabolic process	0.0473822131853775

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	9.41e-25	679
eukaryotic cell	9.41e-25	679
somatic cell	4.40e-14	588
embryonic cell	7.90e-14	250
fibroblast	4.51e-13	76
native cell	8.04e-12	722
mesodermal cell	6.31e-10	121
epithelial cell	8.66e-10	253
non-terminally differentiated cell	2.91e-09	106
muscle precursor cell	1.40e-08	58
myoblast	1.40e-08	58
multi-potent skeletal muscle stem cell	1.40e-08	58
muscle cell	5.33e-08	55
smooth muscle cell	1.42e-07	43
smooth muscle myoblast	1.42e-07	43
contractile cell	2.79e-07	59
vascular associated smooth muscle cell	4.89e-07	32

Uber Anatomy

Ontology term	p-value	n
unilaminar epithelium	2.48e-13	148
trunk	3.66e-12	199
organism subdivision	1.94e-11	264
epithelial tube	2.47e-11	117
mesenchyme	8.42e-11	160
entire embryonic mesenchyme	8.42e-11	160
trunk mesenchyme	2.15e-10	122
splanchnic layer of lateral plate mesoderm	1.44e-08	83
artery	2.58e-08	42
arterial blood vessel	2.58e-08	42
arterial system	2.58e-08	42
vasculature	6.27e-08	78
vascular system	6.27e-08	78
vessel	8.12e-08	68
primordium	3.16e-07	160
immaterial anatomical entity	4.12e-07	117
systemic artery	7.75e-07	33
systemic arterial system	7.75e-07	33

Disease

Ontology term	p-value	n
disease of cellular proliferation	2.84e-09	239
cancer	3.94e-09	235
ovarian cancer	3.69e-07	14

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	14.9754496840058	0.00576829454079388	0.0259457734418352
BHLHE40#8553	2	29.9145423646516	0.00146748352710614	0.00939396335197295
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189163949398788
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00658480394660652
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.03236364081015
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00435463878720525
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.032044815679675
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460124127392436
EP300#2033	3	6.7739417262232	0.00321688050010379	0.016686588981342
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00894883577924663
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00579454098306225
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153642985286604
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127624511859642
IRF3#3661	3	46.9819522114896	9.63568551583244e-06	0.000253040321747052
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156169178310235
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185764854928007
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.0019903133114787
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00244965622199172
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00136042043174738
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00483054332374885
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275448086322241
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245448578152612
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000937615585039036
SREBF1#6720	2	31.3372329603255	0.0013381626513618	0.00887285690721702
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.005406344135039
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189545027519129
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0327970371058782
ZEB1#6935	2	11.2589546783626	0.0101022267664633	0.0377956819366885

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.