Coexpression cluster:C938

Full id: C938_leiomyoma_Smooth_Preadipocyte_hepatic_basal_Adipocyte_Ewing

Phase1 CAGE Peaks

Hg19::chr22:38864041..38864150,+	p1@KDELR3
Hg19::chr2:242212239..242212257,-	p1@HDLBP
Hg19::chr2:47142884..47142955,-	p1@MCFD2
Hg19::chr3:57583064..57583079,-	p1@ARF4
Hg19::chr3:57583085..57583121,-	p2@ARF4
Hg19::chr3:57583130..57583152,-	p3@ARF4
Hg19::chr4:38869366..38869387,+	p3@FAM114A1
Hg19::chr4:38869393..38869404,+	p2@FAM114A1
Hg19::chr4:38869410..38869435,+	p1@FAM114A1

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0016192	vesicle-mediated transport	0.00428373742142871
GO:0015031	protein transport	0.00428373742142871
GO:0045184	establishment of protein localization	0.00428373742142871
GO:0008104	protein localization	0.00428373742142871
GO:0033036	macromolecule localization	0.00428373742142871
GO:0005737	cytoplasm	0.00733327368124839
GO:0006810	transport	0.00972679873071346
GO:0051234	establishment of localization	0.00972679873071346
GO:0046923	ER retention sequence binding	0.00972679873071346
GO:0006621	protein retention in ER	0.0104499899438909
GO:0051179	localization	0.0104499899438909
GO:0005048	signal sequence binding	0.0213109713755608
GO:0032507	maintenance of cellular protein localization	0.0213109713755608
GO:0051651	maintenance of cellular localization	0.0213109713755608
GO:0045185	maintenance of protein localization	0.0213109713755608
GO:0005794	Golgi apparatus	0.0213109713755608
GO:0051235	maintenance of localization	0.0298119136755056
GO:0005793	ER-Golgi intermediate compartment	0.0298119136755056
GO:0005783	endoplasmic reticulum	0.0301261191994913
GO:0044424	intracellular part	0.0342977698170602
GO:0008203	cholesterol metabolic process	0.0462566618772057

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>

---

Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	7.94e-44	180
fibroblast	2.00e-23	75
muscle precursor cell	1.27e-22	57
myoblast	1.27e-22	57
multi-potent skeletal muscle stem cell	1.27e-22	57
mesodermal cell	2.62e-22	119
muscle cell	1.36e-21	54
contractile cell	2.86e-21	59
smooth muscle cell	2.55e-20	42
smooth muscle myoblast	2.55e-20	42
embryonic cell	2.19e-18	248
electrically responsive cell	6.06e-18	60
electrically active cell	6.06e-18	60
vascular associated smooth muscle cell	8.76e-18	32
animal cell	2.73e-13	679
eukaryotic cell	2.73e-13	679
somatic cell	5.70e-13	591
skin fibroblast	1.49e-08	23
preadipocyte	8.43e-08	12
stromal cell	3.26e-07	27

Uber Anatomy

Ontology term	p-value	n
trunk mesenchyme	2.92e-26	143
somite	3.26e-26	83
paraxial mesoderm	3.26e-26	83
presomitic mesoderm	3.26e-26	83
presumptive segmental plate	3.26e-26	83
trunk paraxial mesoderm	3.26e-26	83
presumptive paraxial mesoderm	3.26e-26	83
trunk	2.25e-23	216
dermomyotome	3.61e-23	70
multilaminar epithelium	1.64e-22	82
unilaminar epithelium	1.06e-21	138
vasculature	3.77e-21	79
vascular system	3.77e-21	79
skeletal muscle tissue	7.60e-21	61
striated muscle tissue	7.60e-21	61
myotome	7.60e-21	61
epithelial tube	1.88e-20	118
muscle tissue	3.12e-20	63
musculature	3.12e-20	63
musculature of body	3.12e-20	63
splanchnic layer of lateral plate mesoderm	2.43e-19	84
mesenchyme	3.64e-19	238
entire embryonic mesenchyme	3.64e-19	238
vessel	4.66e-18	69
blood vessel	9.93e-18	60
epithelial tube open at both ends	9.93e-18	60
blood vasculature	9.93e-18	60
vascular cord	9.93e-18	60
artery	1.13e-17	42
arterial blood vessel	1.13e-17	42
arterial system	1.13e-17	42
organism subdivision	3.76e-17	365
multi-cellular organism	2.25e-15	659
systemic artery	1.17e-14	33
systemic arterial system	1.17e-14	33
cardiovascular system	3.68e-14	110
multi-tissue structure	6.38e-14	347
mesoderm	8.09e-14	448
mesoderm-derived structure	8.09e-14	448
presumptive mesoderm	8.09e-14	448
circulatory system	1.16e-13	113
anatomical system	2.18e-12	625
anatomical group	2.42e-12	626
surface structure	7.68e-12	95
cell layer	8.19e-12	312
epithelium	3.17e-11	309
anatomical cluster	6.36e-10	286
integument	1.18e-08	45
integumental system	1.18e-08	45
embryonic structure	5.77e-08	605
developing anatomical structure	5.77e-08	605
anatomical conduit	5.89e-08	241
aorta	7.53e-08	21
aortic system	7.53e-08	21
germ layer	7.59e-08	604
embryonic tissue	7.59e-08	604
presumptive structure	7.59e-08	604
epiblast (generic)	7.59e-08	604
embryo	1.28e-07	612
skin of body	1.82e-07	40

Disease

Ontology term	p-value	n
ovarian cancer	1.25e-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

---

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

---

(#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	7.48772484200292	0.00605035742055281	0.0268411043515893
BATF#10538	3	8.11926726410121	0.00482144889581715	0.0226242216484812
BRCA1#672	3	6.72807688107459	0.00814933356720095	0.0321804389150371
CCNT2#905	8	5.63217917952234	2.97597445628313e-06	0.000101075706094229
CHD2#1106	4	4.59734348182971	0.00737935839755762	0.0304971236469677
CTCFL#140690	3	6.58215811965812	0.00865951196291493	0.032961249722825
E2F1#1869	8	4.3621237465594	2.18983367577486e-05	0.000481380844589036
E2F4#1874	4	5.63024902901531	0.00353657181596461	0.0179473286631452
E2F6#1876	7	3.90223223576463	0.000306742359949273	0.00316341121069835
EGR1#1958	7	3.879694851519	0.000318655785854229	0.00326275408027744
ELK4#2005	4	7.21585851487468	0.00140953905898738	0.00916573375142164
ETS1#2113	7	7.56681405060182	3.61164439627206e-06	0.000118689908465153
GABPB1#2553	5	3.92649102010121	0.00433797609228731	0.0205868080657243
HEY1#23462	9	4.04011104310571	3.4850025352467e-06	0.000116024921829337
HMGN3#9324	7	6.36109267371713	1.17234969197953e-05	0.000298122789093379
MAFF#23764	3	18.7717854966484	0.000433693426399023	0.00404921399603858
MAFK#7975	3	9.03357771260997	0.00356785471281375	0.0180841144553048
MEF2A#4205	3	6.24774363654802	0.0100000500846256	0.0374993799428462
NFYB#4801	3	5.58659775117882	0.0135850027711194	0.0479536318117056
NRF1#4899	4	5.42679086564929	0.00404669891206852	0.0193672984913172
POLR2A#5430	9	2.14745317655807	0.00102941289260802	0.00728936559028337
REST#5978	4	4.28890165161245	0.00945702594596283	0.0356692789010622
RFX5#5993	4	5.35462703430893	0.00424944502767474	0.0202217974778021
SIX5#147912	3	5.695571785153	0.0128879469903482	0.0463563953617915
SRF#6722	6	9.1981188414452	1.00386889165062e-05	0.000263094261418065
TAF1#6872	9	3.34304628574529	1.91655056102793e-05	0.000433627868377809
TFAP2C#7022	4	4.80410160438232	0.00629930343474712	0.0277885090357573
THAP1#55145	3	10.4563815342838	0.00235392350402662	0.0133413695575534
ZBTB7A#51341	5	4.08439405993105	0.00363499031283399	0.0183753510785126
ZEB1#6935	3	5.62947733918129	0.0133048823634195	0.047039560228611

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

---

This analysis result is provided for C0 - C305 clusters.