Coexpression cluster:C1085

Full id: C1085_liposarcoma_placenta_Olfactory_amniotic_Hair_mesothelioma_Smooth

Phase1 CAGE Peaks

Hg19::chr5:95066730..95066782,+	p4@RHOBTB3
Hg19::chr5:95066823..95066879,+	p2@RHOBTB3
Hg19::chr5:95067004..95067024,+	p5@RHOBTB3
Hg19::chr5:95067025..95067058,+	p1@RHOBTB3
Hg19::chr5:95067060..95067082,+	p3@RHOBTB3
Hg19::chr5:95067089..95067108,+	p6@RHOBTB3
Hg19::chr5:95067128..95067139,+	p8@RHOBTB3
Hg19::chr5:95067165..95067168,+	p12@RHOBTB3

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	1.39e-24	180
muscle precursor cell	1.85e-15	57
myoblast	1.85e-15	57
multi-potent skeletal muscle stem cell	1.85e-15	57
muscle cell	1.54e-14	54
contractile cell	2.39e-13	59
electrically responsive cell	3.44e-12	60
electrically active cell	3.44e-12	60
smooth muscle cell	1.05e-11	42
smooth muscle myoblast	1.05e-11	42
fibroblast	4.16e-11	75
vascular associated smooth muscle cell	2.97e-08	32
mesodermal cell	1.22e-07	119
fat cell	3.85e-07	15

Uber Anatomy

Ontology term	p-value	n
organism subdivision	1.92e-24	365
multi-tissue structure	1.69e-19	347
cell layer	3.26e-17	312
epithelium	6.07e-17	309
anatomical cluster	1.55e-16	286
skeletal muscle tissue	2.72e-15	61
striated muscle tissue	2.72e-15	61
myotome	2.72e-15	61
somite	6.32e-15	83
paraxial mesoderm	6.32e-15	83
presomitic mesoderm	6.32e-15	83
presumptive segmental plate	6.32e-15	83
trunk paraxial mesoderm	6.32e-15	83
presumptive paraxial mesoderm	6.32e-15	83
muscle tissue	8.84e-15	63
musculature	8.84e-15	63
musculature of body	8.84e-15	63
anatomical conduit	2.77e-14	241
dermomyotome	5.71e-14	70
multi-cellular organism	1.18e-13	659
tube	1.54e-13	194
trunk mesenchyme	2.00e-13	143
regional part of nervous system	1.27e-12	94
nervous system	1.27e-12	94
head	8.22e-12	123
brain	1.45e-11	69
future brain	1.45e-11	69
central nervous system	1.59e-11	82
regional part of brain	4.46e-11	59
anatomical system	1.75e-10	625
anterior region of body	2.01e-10	129
craniocervical region	2.01e-10	129
trunk	2.06e-10	216
neural plate	2.25e-10	86
presumptive neural plate	2.25e-10	86
ectoderm-derived structure	2.53e-10	169
anatomical group	2.62e-10	626
multilaminar epithelium	4.08e-10	82
unilaminar epithelium	4.33e-10	138
neural tube	4.48e-10	57
neural rod	4.48e-10	57
future spinal cord	4.48e-10	57
neural keel	4.48e-10	57
ectoderm	1.13e-09	173
presumptive ectoderm	1.13e-09	173
neurectoderm	2.20e-09	90
embryonic structure	8.32e-09	605
developing anatomical structure	8.32e-09	605
germ layer	8.67e-09	604
embryonic tissue	8.67e-09	604
presumptive structure	8.67e-09	604
epiblast (generic)	8.67e-09	604
pre-chordal neural plate	1.46e-08	61
embryo	2.27e-08	612
regional part of forebrain	4.33e-08	41
forebrain	4.33e-08	41
future forebrain	4.33e-08	41
organ part	4.98e-08	219
anterior neural tube	5.59e-08	42
telencephalon	1.62e-07	34
splanchnic layer of lateral plate mesoderm	1.89e-07	84
regional part of telencephalon	2.82e-07	33
gray matter	3.07e-07	34
brain grey matter	3.07e-07	34
epithelial tube	3.34e-07	118
organ	6.71e-07	511
mesenchyme	7.37e-07	238
entire embryonic mesenchyme	7.37e-07	238
cerebral hemisphere	7.48e-07	32

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
BHLHE40#8553	7	39.2628368536052	2.13093689260982e-11	2.55221236384492e-09
CCNT2#905	8	6.33620157696263	3.84606837428661e-07	1.87613047614255e-05
CTBP2#1488	8	62.7170003393281	4.13860279872435e-15	7.33839622573807e-13
CTCF#10664	7	4.69022432644065	5.26249365325459e-05	0.000893819441620193
E2F1#1869	8	4.90738921487932	2.97124777369457e-06	0.0001015425871194
E2F6#1876	7	4.39001126523521	8.25033297218753e-05	0.00124032895535093
EBF1#1879	7	7.79315849074788	1.62130676909081e-06	6.14842620396063e-05
EGR1#1958	7	4.36465670795887	8.58120841941444e-05	0.00128636834522065
EP300#2033	8	6.7739417262232	2.25366016107097e-07	1.19114379333042e-05
ETS1#2113	7	8.51266580692704	8.8174082362229e-07	3.82425788531098e-05
GATA1#2623	8	13.5603081438004	8.7300552826276e-10	8.1845443775794e-08
HEY1#23462	8	4.04011104310571	1.4081650274634e-05	0.000339177461492736
HMGN3#9324	8	8.17854772335059	4.99020179935884e-08	3.19541192963359e-06
IRF1#3659	8	7.6371637535639	8.63190100943299e-08	5.13094541561851e-06
JUNB#3726	8	30.6106326598211	1.29143502615752e-12	1.79595449662937e-10
MAX#4149	7	5.64598607038123	1.48396919857828e-05	0.000351917027997995
MYC#4609	8	5.2222818716094	1.80650725138099e-06	6.77206786887938e-05
POLR2A#5430	8	2.14745317655807	0.00221072578897191	0.0127244965926942
RAD21#5885	7	9.06065465852429	5.73112922357867e-07	2.63912436058789e-05
REST#5978	5	6.03126794758001	0.000510547353254391	0.00442976281685929
SIN3A#25942	8	5.40888472681514	1.36410592556506e-06	5.35585935188305e-05
SMC3#9126	5	9.40308302808303	6.12099279950925e-05	0.00100387934514439
SP1#6667	6	4.27378603360567	0.000590472686428894	0.00494414951478772
STAT1#6772	8	20.7065874971992	2.95008695392417e-11	3.42337923756541e-09
TAF1#6872	8	3.34304628574529	6.40776711117462e-05	0.00104386334319758
TBP#6908	8	3.70677068709639	2.80450451364125e-05	0.00059231475611765
TCF12#6938	7	9.30515678941312	4.76792693502233e-07	2.25014695511431e-05
TCF7L2#6934	8	10.7701765631373	5.51536816569572e-09	4.40045481938193e-07
TFAP2A#7020	8	16.518634373045	1.79963993911652e-10	1.88140736337728e-08
TFAP2C#7022	8	10.8092286098602	5.35792840387033e-09	4.28794394307903e-07
USF1#7391	8	6.36149927720796	3.72538670743375e-07	1.83266915844406e-05
ZBTB7A#51341	8	7.3519093078759	1.17052559937328e-07	6.76527521156316e-06
ZNF263#10127	8	8.22184163701068	4.78378813558924e-08	3.10512149840152e-06

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.