Coexpression cluster:C2895

Full id: C2895_immature_Mallassezderived_mesenchymal_CD14_Fibroblast_migratory_Endothelial

Phase1 CAGE Peaks

Hg19::chr7:39663146..39663225,+	p1@RALA
Hg19::chr7:39663255..39663276,+	p3@RALA
Hg19::chr7:39663286..39663317,+	p2@RALA
Hg19::chr7:39663534..39663558,+	p5@RALA

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

---

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>disease_data<br>

---

Cell Type

Ontology term	p-value	n
mesodermal cell	7.98e-19	119
somatic cell	3.67e-16	591
animal cell	7.23e-16	679
eukaryotic cell	7.23e-16	679
non-terminally differentiated cell	6.53e-14	180
endothelial cell of vascular tree	1.44e-13	24
endothelial cell	2.00e-12	35
somatic stem cell	3.31e-12	436
multi fate stem cell	3.66e-12	430
stem cell	1.56e-11	444
muscle precursor cell	7.28e-11	57
myoblast	7.28e-11	57
multi-potent skeletal muscle stem cell	7.28e-11	57
vascular associated smooth muscle cell	9.59e-11	32
blood vessel endothelial cell	1.08e-10	18
embryonic blood vessel endothelial progenitor cell	1.08e-10	18
embryonic cell	2.11e-10	248
fibroblast	2.22e-10	75
muscle cell	3.28e-10	54
native cell	3.35e-10	722
lining cell	8.60e-10	57
barrier cell	8.60e-10	57
meso-epithelial cell	1.51e-09	44
smooth muscle cell	2.22e-09	42
smooth muscle myoblast	2.22e-09	42
CD14-positive, CD16-negative classical monocyte	3.82e-09	42
electrically responsive cell	4.98e-09	60
electrically active cell	4.98e-09	60
contractile cell	4.00e-08	59
classical monocyte	9.68e-08	45
cardiocyte	8.01e-07	16
macrophage dendritic cell progenitor	8.11e-07	65

Uber Anatomy

Ontology term	p-value	n
vessel	9.44e-21	69
blood vessel	2.92e-19	60
epithelial tube open at both ends	2.92e-19	60
blood vasculature	2.92e-19	60
vascular cord	2.92e-19	60
vasculature	3.70e-19	79
vascular system	3.70e-19	79
splanchnic layer of lateral plate mesoderm	7.01e-18	84
artery	3.00e-17	42
arterial blood vessel	3.00e-17	42
arterial system	3.00e-17	42
systemic artery	1.86e-13	33
systemic arterial system	1.86e-13	33
cardiovascular system	1.09e-12	110
musculoskeletal system	3.43e-12	167
circulatory system	2.72e-11	113
somite	5.22e-11	83
paraxial mesoderm	5.22e-11	83
presomitic mesoderm	5.22e-11	83
presumptive segmental plate	5.22e-11	83
trunk paraxial mesoderm	5.22e-11	83
presumptive paraxial mesoderm	5.22e-11	83
endothelium	1.08e-10	18
blood vessel endothelium	1.08e-10	18
cardiovascular system endothelium	1.08e-10	18
aorta	3.96e-10	21
aortic system	3.96e-10	21
epithelial tube	2.51e-09	118
dermomyotome	2.72e-09	70
mesoderm	3.70e-09	448
mesoderm-derived structure	3.70e-09	448
presumptive mesoderm	3.70e-09	448
simple squamous epithelium	5.79e-09	22
multilaminar epithelium	7.10e-09	82
skeletal muscle tissue	7.26e-09	61
striated muscle tissue	7.26e-09	61
myotome	7.26e-09	61
muscle tissue	1.58e-08	63
musculature	1.58e-08	63
musculature of body	1.58e-08	63
anatomical system	4.43e-08	625
lateral plate mesoderm	6.09e-08	216
anatomical group	6.19e-08	626
squamous epithelium	9.35e-08	25
unilaminar epithelium	1.77e-07	138
multi-cellular organism	7.82e-07	659

Disease

Ontology term	p-value	n
ovarian cancer	1.02e-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
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00513673978931347
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00999375616041047
EBF1#1879	3	6.67985013492675	0.00518429411827891	0.0240641108186192
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.016127018762483
ETS1#2113	3	7.29657069165175	0.0040085737751139	0.0192130076410794
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.00390878211137204
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186631944458037
HMGN3#9324	3	6.13391079251294	0.00664069668332472	0.0283161605728065
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.00308039916205958
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.0076941795672089
NR2C2#7182	4	32.6146109052409	8.82887529809196e-07	3.82446664146589e-05
POU2F2#5452	3	6.82959304330689	0.00486047377520374	0.0227766420159063
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00798133950706665
SIX5#147912	4	17.086715355459	1.17257016123224e-05	0.000297816281782426
TAF7#6879	3	8.57480205369294	0.0025005543351524	0.0140406125918807
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0245059543947485
TCF7L2#6934	4	10.7701765631373	7.42969445082454e-05	0.00115778850902665
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00509144203078231
ZBTB7A#51341	3	5.51393198090692	0.00903835282108109	0.0342621512932702
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00249971642345592

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.