Coexpression cluster:C4304

Full id: C4304_iPS_H9_Lens_HES3GFP_Ciliary_renal_Fibroblast

Phase1 CAGE Peaks

Hg19::chr3:170076223..170076242,+	p6@SKIL
Hg19::chr3:170076246..170076261,+	p8@SKIL
Hg19::chr3:170076314..170076334,+	p2@SKIL

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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No GOStat results

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
animal cell	2.59e-14	679
eukaryotic cell	2.59e-14	679
mesodermal cell	8.18e-12	119
non-terminally differentiated cell	2.10e-10	180
embryonic cell	3.78e-10	248
somatic cell	1.47e-09	591
electrically responsive cell	1.98e-09	60
electrically active cell	1.98e-09	60
muscle precursor cell	5.37e-09	57
myoblast	5.37e-09	57
multi-potent skeletal muscle stem cell	5.37e-09	57
muscle cell	5.54e-08	54
contractile cell	8.77e-08	59

Uber Anatomy

Ontology term	p-value	n
artery	4.32e-12	42
arterial blood vessel	4.32e-12	42
arterial system	4.32e-12	42
systemic artery	1.38e-11	33
systemic arterial system	1.38e-11	33
epithelial tube	3.96e-11	118
splanchnic layer of lateral plate mesoderm	6.28e-09	84
vasculature	6.30e-09	79
vascular system	6.30e-09	79
blood vessel	1.59e-08	60
epithelial tube open at both ends	1.59e-08	60
blood vasculature	1.59e-08	60
vascular cord	1.59e-08	60
aorta	1.66e-08	21
aortic system	1.66e-08	21
unilaminar epithelium	7.61e-08	138
mesoderm	7.83e-08	448
mesoderm-derived structure	7.83e-08	448
presumptive mesoderm	7.83e-08	448
cardiovascular system	9.32e-08	110
vessel	1.83e-07	69
circulatory system	2.31e-07	113
skeletal muscle tissue	5.43e-07	61
striated muscle tissue	5.43e-07	61
myotome	5.43e-07	61

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.019061317870885
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115540555823638
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280449654168969
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326614987499662
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321640506337993
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463815975074847
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167950301214927
ESR1#2099	3	30.7686032961545	3.43136389821584e-05	0.000678342256607541
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108955566023224
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157198935925304
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270296649031076
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173394000844972
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.0066633414485695
REST#5978	3	9.65002871612802	0.00111263624711459	0.0076970667690535
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165629417171346
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203502876942599
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00309962263524279
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00617488495612458
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330428827421428
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.014059988539512

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.