Coexpression cluster:C4288

Full id: C4288_Fibroblast_amniotic_Smooth_Synoviocyte_salivary_gastric_Chondrocyte

Phase1 CAGE Peaks

Hg19::chr3:14166542..14166566,+	p3@TMEM43
Hg19::chr3:14166567..14166598,+	p2@TMEM43
Hg19::chr3:14166625..14166649,+	p1@TMEM43

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	1.19e-21	180
fibroblast	9.75e-19	75
somatic cell	2.68e-13	591
animal cell	1.24e-12	679
eukaryotic cell	1.24e-12	679
skin fibroblast	3.63e-10	23
mesodermal cell	4.66e-09	119
embryonic cell	2.78e-08	248
fat cell	7.66e-08	15
contractile cell	2.32e-07	59
muscle precursor cell	3.28e-07	57
myoblast	3.28e-07	57
multi-potent skeletal muscle stem cell	3.28e-07	57
muscle cell	6.89e-07	54

Uber Anatomy

Ontology term	p-value	n
surface structure	1.90e-13	95
mesoderm	7.74e-12	448
mesoderm-derived structure	7.74e-12	448
presumptive mesoderm	7.74e-12	448
multi-cellular organism	8.20e-11	659
integument	9.78e-10	45
integumental system	9.78e-10	45
splanchnic layer of lateral plate mesoderm	1.59e-09	84
somite	2.93e-09	83
paraxial mesoderm	2.93e-09	83
presomitic mesoderm	2.93e-09	83
presumptive segmental plate	2.93e-09	83
trunk paraxial mesoderm	2.93e-09	83
presumptive paraxial mesoderm	2.93e-09	83
multilaminar epithelium	6.61e-09	82
skin of body	7.06e-09	40
anatomical system	2.21e-08	625
trunk	2.57e-08	216
anatomical group	3.82e-08	626
dermomyotome	5.06e-08	70
organ component layer	7.36e-08	57
vasculature	1.08e-07	79
vascular system	1.08e-07	79
skeletal muscle tissue	2.76e-07	61
striated muscle tissue	2.76e-07	61
myotome	2.76e-07	61
muscle tissue	3.42e-07	63
musculature	3.42e-07	63
musculature of body	3.42e-07	63
trunk mesenchyme	4.29e-07	143
artery	4.74e-07	42
arterial blood vessel	4.74e-07	42
arterial system	4.74e-07	42
blood vessel	5.92e-07	60
epithelial tube open at both ends	5.92e-07	60
blood vasculature	5.92e-07	60
vascular cord	5.92e-07	60
vessel	6.56e-07	69
extraembryonic membrane	8.52e-07	14
membranous layer	8.52e-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	3	22.4631745260087	8.81932387510763e-05	0.0012987610916418
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164358575924802
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190586630912372
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115534081512541
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00661945351483745
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280414860365466
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326554637354152
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00438063663071096
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323380575110091
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321603625188315
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.046373647012523
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00763920871872467
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.015453397172236
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108949347453164
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128442617704896
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00445267343430524
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157190838313604
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187061096697235
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00721711907211526
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295355635626257
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000739488732498627
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00472368437280844
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173359841270338
REST#5978	3	9.65002871612802	0.00111263624711459	0.0076960472224916
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027762654916472
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00240080384718557
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00644290629298315
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00248897862333035
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00617396278095192
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00422442772487097
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330379297149377
ZBTB33#10009	3	31.6647250299812	3.14815888737575e-05	0.000634363430520232
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00389995668686085

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.