Coexpression cluster:C2089

Full id: C2089_pharyngeal_epidermoid_Hep2_rectal_Prostate_gastric_Adipocyte

Phase1 CAGE Peaks

Hg19::chr11:101980713..101980754,+	p8@YAP1
Hg19::chr11:101981327..101981348,+	p7@YAP1
Hg19::chr11:101981353..101981380,+	p5@YAP1
Hg19::chr11:101981423..101981503,+	p3@YAP1

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
non-terminally differentiated cell	3.77e-13	180
fibroblast	9.90e-10	75
epithelial cell	1.76e-08	254

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	1.00e-16	169
endoderm	1.00e-16	169
presumptive endoderm	1.00e-16	169
multi-tissue structure	1.87e-15	347
digestive system	3.83e-15	155
digestive tract	3.83e-15	155
primitive gut	3.83e-15	155
mesenchyme	5.08e-15	238
entire embryonic mesenchyme	5.08e-15	238
multi-cellular organism	1.65e-13	659
trunk	9.24e-12	216
mixed endoderm/mesoderm-derived structure	6.67e-11	130
organism subdivision	5.42e-10	365
subdivision of digestive tract	1.01e-09	129
endodermal part of digestive tract	1.01e-09	129
organ component layer	3.40e-09	57
organ	3.83e-09	511
reproductive structure	4.98e-09	59
reproductive system	4.98e-09	59
primordium	5.79e-09	168
surface structure	8.72e-09	95
embryo	1.55e-08	612
trunk mesenchyme	2.25e-08	143
anatomical system	2.46e-08	625
anatomical group	3.48e-08	626
larynx	1.18e-07	9
organ part	3.64e-07	219
reproductive organ	3.66e-07	48
orifice	5.15e-07	35
embryonic structure	5.65e-07	605
developing anatomical structure	5.65e-07	605
germ layer	9.97e-07	604
embryonic tissue	9.97e-07	604
presumptive structure	9.97e-07	604
epiblast (generic)	9.97e-07	604

Disease

Ontology term	p-value	n
cell type cancer	1.68e-09	143
carcinoma	2.25e-08	106

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	2	22.4359067734887	0.00289146449685312	0.0156361860190982
E2F4#1874	3	9.50104523646333	0.00185075103472827	0.010923457887312
EP300#2033	3	5.0804562946674	0.0114429840539824	0.0418655437404143
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378360690173517
GATA3#2625	3	20.4273872679045	0.000192441557625832	0.00231868987504433
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185475043652472
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0465874257318082
STAT3#6774	3	7.88959874786568	0.00319076048168013	0.0167373095904667
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321158345377392
TCF7L2#6934	3	8.07763242235301	0.00297838168583462	0.0158558061416496
TFAP2A#7020	4	16.518634373045	1.34240829060362e-05	0.00032581868338915
TFAP2C#7022	4	10.8092286098602	7.32289634782688e-05	0.00114336368914739
TRIM28#10155	4	18.5905250452625	8.36730015875654e-06	0.000229664247379862

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.