Coexpression cluster:C1682

Full id: C1682_schwannoma_Fibroblast_hepatoblastoma_Wilms_adrenal_Aortic_meningioma

Phase1 CAGE Peaks

Hg19::chr12:66218836..66218888,+	p1@HMGA2
Hg19::chr12:66218904..66218913,+	p11@HMGA2
Hg19::chr12:66218923..66218934,+	p14@HMGA2
Hg19::chr12:66357214..66357233,+	p13@HMGA2
Hg19::chr12:66358080..66358094,+	p15@HMGA2

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><br>

---

Cell Type

Ontology term	p-value	n
embryonic cell	2.63e-31	248
non-terminally differentiated cell	5.71e-31	180
animal cell	3.84e-20	679
eukaryotic cell	3.84e-20	679
muscle precursor cell	7.59e-20	57
myoblast	7.59e-20	57
multi-potent skeletal muscle stem cell	7.59e-20	57
electrically responsive cell	8.86e-19	60
electrically active cell	8.86e-19	60
muscle cell	3.16e-18	54
contractile cell	4.93e-18	59
somatic cell	6.81e-18	591
mesodermal cell	2.83e-17	119
smooth muscle cell	2.21e-16	42
smooth muscle myoblast	2.21e-16	42
vascular associated smooth muscle cell	3.74e-14	32
epithelial cell	1.77e-13	254
fibroblast	5.31e-10	75
native cell	1.14e-09	722
endo-epithelial cell	4.52e-09	43
endodermal cell	1.13e-08	59

Uber Anatomy

Ontology term	p-value	n
multilaminar epithelium	3.79e-22	82
somite	4.10e-22	83
paraxial mesoderm	4.10e-22	83
presomitic mesoderm	4.10e-22	83
presumptive segmental plate	4.10e-22	83
trunk paraxial mesoderm	4.10e-22	83
presumptive paraxial mesoderm	4.10e-22	83
trunk mesenchyme	6.94e-21	143
dermomyotome	2.00e-19	70
unilaminar epithelium	6.08e-19	138
skeletal muscle tissue	1.84e-17	61
striated muscle tissue	1.84e-17	61
myotome	1.84e-17	61
muscle tissue	1.51e-16	63
musculature	1.51e-16	63
musculature of body	1.51e-16	63
vasculature	2.84e-16	79
vascular system	2.84e-16	79
epithelial tube	2.34e-15	118
trunk	2.60e-15	216
artery	2.53e-14	42
arterial blood vessel	2.53e-14	42
arterial system	2.53e-14	42
mesenchyme	4.16e-14	238
entire embryonic mesenchyme	4.16e-14	238
blood vessel	4.06e-13	60
epithelial tube open at both ends	4.06e-13	60
blood vasculature	4.06e-13	60
vascular cord	4.06e-13	60
splanchnic layer of lateral plate mesoderm	1.40e-12	84
vessel	1.74e-12	69
cell layer	2.44e-12	312
multi-tissue structure	4.57e-12	347
epithelium	8.76e-12	309
systemic artery	2.73e-11	33
systemic arterial system	2.73e-11	33
organism subdivision	3.71e-11	365
cardiovascular system	3.26e-10	110
multi-cellular organism	6.42e-10	659
circulatory system	2.64e-09	113
surface structure	5.33e-09	95
embryo	1.18e-08	612
anatomical system	4.01e-08	625
anatomical group	6.45e-08	626
aorta	1.52e-07	21
aortic system	1.52e-07	21
embryonic structure	1.60e-07	605
developing anatomical structure	1.60e-07	605
germ layer	1.64e-07	604
embryonic tissue	1.64e-07	604
presumptive structure	1.64e-07	604
epiblast (generic)	1.64e-07	604
mesoderm	2.21e-07	448
mesoderm-derived structure	2.21e-07	448
presumptive mesoderm	2.21e-07	448
subdivision of head	3.39e-07	48

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
CTCF#10664	4	4.28820509846002	0.00515201558824328	0.0239249157857065
JUNB#3726	3	18.3663795958927	0.000331631981170089	0.00337773673507148
TCF7L2#6934	3	6.46210593788241	0.00693010875568919	0.0293156315904015
TFAP2C#7022	3	6.48553716591613	0.00685895151794	0.029055813968611
ZZZ3#26009	3	143.64792746114	7.21371177912933e-07	3.21550509816683e-05

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.