Coexpression cluster:C3065

Full id: C3065_anaplastic_Prostate_iPS_HES3GFP_Urothelial_Alveolar_H9

Phase1 CAGE Peaks

Hg19::chr10:99185919..99185956,+	p2@PGAM1
Hg19::chr10:99185961..99185987,+	p3@PGAM1
Hg19::chr10:99185993..99186014,+	p1@PGAM1

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
non-terminally differentiated cell	1.42e-15	180
embryonic cell	4.24e-14	248
animal cell	2.07e-13	679
eukaryotic cell	2.07e-13	679
vascular associated smooth muscle cell	3.37e-10	32
contractile cell	6.18e-10	59
smooth muscle cell	6.96e-10	42
smooth muscle myoblast	6.96e-10	42
muscle precursor cell	7.00e-10	57
myoblast	7.00e-10	57
multi-potent skeletal muscle stem cell	7.00e-10	57
electrically responsive cell	7.40e-10	60
electrically active cell	7.40e-10	60
epithelial cell	3.77e-09	254
muscle cell	4.19e-09	54
mesodermal cell	5.57e-09	119
somatic cell	7.04e-09	591

Uber Anatomy

Ontology term	p-value	n
multilaminar epithelium	3.01e-10	82
cell layer	1.30e-09	312
artery	2.02e-09	42
arterial blood vessel	2.02e-09	42
arterial system	2.02e-09	42
epithelium	3.49e-09	309
dermomyotome	6.45e-09	70
somite	8.53e-09	83
paraxial mesoderm	8.53e-09	83
presomitic mesoderm	8.53e-09	83
presumptive segmental plate	8.53e-09	83
trunk paraxial mesoderm	8.53e-09	83
presumptive paraxial mesoderm	8.53e-09	83
organism subdivision	3.87e-08	365
skeletal muscle tissue	1.91e-07	61
striated muscle tissue	1.91e-07	61
myotome	1.91e-07	61
trunk mesenchyme	3.37e-07	143
systemic artery	4.88e-07	33
systemic arterial system	4.88e-07	33
muscle tissue	8.68e-07	63
musculature	8.68e-07	63
musculature of body	8.68e-07	63
organ part	8.77e-07	219

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	3	22.4631745260087	8.81932387510763e-05	0.00129238300293583
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189102954067552
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00658342550742992
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278205872830482
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171040204197475
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323529765562309
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00435353148797135
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320348843069002
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319018602684432
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460014592657127
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0166832745332377
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185702732150227
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293182687327367
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268561694982035
NR2C2#7182	3	32.6146109052409	2.88098172333076e-05	0.000603705558192098
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00469353566312191
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172248505855294
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245416558944261
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0327872793500358
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00387608739865224
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.010893457127909

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.