Coexpression cluster:C3634

Full id: C3634_testicular_Trabecular_osteosarcoma_gastric_Fibroblast_teratocarcinoma_lung

Phase1 CAGE Peaks

Hg19::chr17:41622982..41623001,-	p11@ETV4
Hg19::chr17:41623009..41623053,-	p4@ETV4
Hg19::chr17:41623075..41623101,-	p9@ETV4

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	3.60e-32	254
embryonic cell	8.27e-24	248
animal cell	5.83e-21	679
eukaryotic cell	5.83e-21	679
non-terminally differentiated cell	3.79e-11	180
mesodermal cell	3.92e-10	119
native cell	5.44e-10	722
squamous epithelial cell	6.71e-09	62
endodermal cell	1.41e-07	59
contractile cell	2.44e-07	59
somatic cell	3.54e-07	591
electrically responsive cell	5.74e-07	60
electrically active cell	5.74e-07	60

Uber Anatomy

Ontology term	p-value	n
mesenchyme	3.34e-15	238
entire embryonic mesenchyme	3.34e-15	238
cell layer	4.42e-14	312
epithelial tube	1.63e-13	118
trunk	2.14e-13	216
trunk mesenchyme	2.94e-13	143
epithelium	3.32e-13	309
unilaminar epithelium	7.35e-13	138
multi-tissue structure	8.49e-12	347
primordium	3.03e-10	168
immaterial anatomical entity	5.58e-10	126
trunk region element	4.14e-09	107
endoderm-derived structure	6.67e-09	169
endoderm	6.67e-09	169
presumptive endoderm	6.67e-09	169
vasculature	6.84e-09	79
vascular system	6.84e-09	79
anatomical space	1.11e-08	104
blood vessel	2.15e-08	60
epithelial tube open at both ends	2.15e-08	60
blood vasculature	2.15e-08	60
vascular cord	2.15e-08	60
organism subdivision	2.46e-08	365
multilaminar epithelium	5.19e-08	82
vessel	8.04e-08	69
artery	9.40e-08	42
arterial blood vessel	9.40e-08	42
arterial system	9.40e-08	42
splanchnic layer of lateral plate mesoderm	9.68e-08	84
digestive system	2.83e-07	155
digestive tract	2.83e-07	155
primitive gut	2.83e-07	155
somite	3.12e-07	83
paraxial mesoderm	3.12e-07	83
presomitic mesoderm	3.12e-07	83
presumptive segmental plate	3.12e-07	83
trunk paraxial mesoderm	3.12e-07	83
presumptive paraxial mesoderm	3.12e-07	83
mixed endoderm/mesoderm-derived structure	6.82e-07	130

Disease

Ontology term	p-value	n
carcinoma	5.82e-12	106
cancer	7.51e-12	235
cell type cancer	1.11e-11	143
disease of cellular proliferation	1.64e-11	239

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	3	44.8718135469774	1.10603738662898e-05	0.000284375772087996
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.018982872606365
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00659954329511599
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279145022374432
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324897730965635
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321694794247817
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320220568039347
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167322965561203
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00242763471365441
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00580769743727339
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153946848794509
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00390868564569493
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00122734771048847
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.000756347487707897
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.0016516309426659
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276324611656599
SP1#6667	3	5.6983813781409	0.00540396270171217	0.024620881237365
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00612923848077604
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328937077249128
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.013999320572769

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.