Coexpression cluster:C749

Full id: C749_Wilms_rhabdomyosarcoma_medulloblastoma_fibrous_retinoblastoma_endometrial_schwannoma

Phase1 CAGE Peaks

Hg19::chr12:66218152..66218174,+	p10@HMGA2
Hg19::chr12:66218183..66218209,+	p4@HMGA2
Hg19::chr12:66218212..66218244,+	p5@HMGA2
Hg19::chr12:66218255..66218304,+	p3@HMGA2
Hg19::chr12:66218378..66218401,+	p6@HMGA2
Hg19::chr12:66218413..66218418,+	p17@HMGA2
Hg19::chr12:66218420..66218439,+	p12@HMGA2
Hg19::chr12:66218443..66218461,+	p8@HMGA2
Hg19::chr12:66218469..66218477,+	p16@HMGA2
Hg19::chr12:66218573..66218596,+	p7@HMGA2
Hg19::chr12:66218598..66218645,+	p2@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

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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
embryonic cell	4.37e-30	248
non-terminally differentiated cell	2.59e-27	180
epithelial cell	4.40e-18	254
animal cell	5.41e-18	679
eukaryotic cell	5.41e-18	679
somatic cell	4.53e-15	591
mesodermal cell	1.32e-13	119
contractile cell	1.52e-13	59
muscle precursor cell	3.06e-13	57
myoblast	3.06e-13	57
multi-potent skeletal muscle stem cell	3.06e-13	57
electrically responsive cell	5.35e-13	60
electrically active cell	5.35e-13	60
muscle cell	3.24e-12	54
fibroblast	6.33e-10	75
smooth muscle cell	3.99e-09	42
smooth muscle myoblast	3.99e-09	42
endodermal cell	1.20e-08	59
endo-epithelial cell	2.23e-08	43
native cell	2.26e-08	722
vascular associated smooth muscle cell	9.72e-08	32

Uber Anatomy

Ontology term	p-value	n
trunk mesenchyme	2.25e-19	143
multilaminar epithelium	1.25e-16	82
somite	4.34e-16	83
paraxial mesoderm	4.34e-16	83
presomitic mesoderm	4.34e-16	83
presumptive segmental plate	4.34e-16	83
trunk paraxial mesoderm	4.34e-16	83
presumptive paraxial mesoderm	4.34e-16	83
cell layer	7.45e-16	312
trunk	8.37e-16	216
unilaminar epithelium	1.61e-15	138
epithelium	6.78e-15	309
organism subdivision	1.50e-14	365
epithelial tube	4.68e-14	118
multi-tissue structure	6.80e-14	347
mesenchyme	8.79e-14	238
entire embryonic mesenchyme	8.79e-14	238
dermomyotome	1.46e-13	70
vasculature	1.08e-12	79
vascular system	1.08e-12	79
multi-cellular organism	2.33e-11	659
skeletal muscle tissue	3.29e-11	61
striated muscle tissue	3.29e-11	61
myotome	3.29e-11	61
muscle tissue	1.43e-10	63
musculature	1.43e-10	63
musculature of body	1.43e-10	63
embryo	7.17e-10	612
surface structure	1.45e-09	95
blood vessel	3.52e-09	60
epithelial tube open at both ends	3.52e-09	60
blood vasculature	3.52e-09	60
vascular cord	3.52e-09	60
subdivision of head	5.11e-09	48
vessel	7.57e-09	69
anatomical system	8.43e-09	625
anatomical group	1.39e-08	626
artery	1.75e-08	42
arterial blood vessel	1.75e-08	42
arterial system	1.75e-08	42
embryonic structure	2.00e-08	605
developing anatomical structure	2.00e-08	605
germ layer	2.03e-08	604
embryonic tissue	2.03e-08	604
presumptive structure	2.03e-08	604
epiblast (generic)	2.03e-08	604
splanchnic layer of lateral plate mesoderm	2.57e-08	84
ectodermal placode	4.81e-08	29
camera-type eye	7.10e-08	19
simple eye	7.10e-08	19
ocular region	7.10e-08	19
optic cup	7.10e-08	19
eye primordium	7.10e-08	19
optic vesicle	7.10e-08	19
eye	2.20e-07	20
cardiovascular system	4.37e-07	110
face	5.38e-07	21

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	4	16.3170231079918	7.16950673576926e-05	0.0011276748704473
CTCF#10664	10	4.87296033915911	4.65999095504339e-07	2.20418838475442e-05
E2F1#1869	11	4.90738921487932	2.51269297258347e-08	1.75416538344683e-06
HEY1#23462	11	4.04011104310571	2.1344242734918e-07	1.13733233009801e-05
HNF4G#3174	4	10.455790009617	0.000396230217565117	0.00387434581895733
JUND#3727	7	4.45114978119065	0.000236377425785552	0.00257532046438736
NR3C1#2908	11	14.973023331173	1.17432722508375e-13	1.82780269836844e-11
POLR2A#5430	11	2.14745317655807	0.000223198342238743	0.00248487492432279
TAF1#6872	11	3.34304628574529	1.71447392661505e-06	6.47821788790697e-05
TCF7L2#6934	6	5.87464176171128	0.000195714842587612	0.00235432647373964
TFAP2C#7022	10	9.8265714635093	4.61610782404372e-10	4.48884250498419e-08
ZNF263#10127	11	8.22184163701068	8.59817612641675e-11	9.4128397952499e-09
ZZZ3#26009	7	152.353862458785	7.02064328878409e-15	1.22408842143126e-12

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.