Coexpression cluster:C3068

Full id: C3068_epidermoid_pharyngeal_aorta_amniotic_chorionic_Hep2_mature

Phase1 CAGE Peaks

Hg19::chr11:101980791..101980865,+	p4@YAP1
Hg19::chr11:101981127..101981164,+	p2@YAP1
Hg19::chr11:101981169..101981187,+	p1@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><br>

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Cell Type

Ontology term	p-value	n
fibroblast	9.20e-13	76
endodermal cell	1.62e-08	58
epithelial cell	1.60e-07	253
skin fibroblast	1.82e-07	23

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	2.53e-22	160
endoderm	2.53e-22	160
presumptive endoderm	2.53e-22	160
digestive system	1.39e-19	145
digestive tract	1.39e-19	145
primitive gut	1.39e-19	145
multi-tissue structure	1.05e-16	342
surface structure	1.19e-16	99
organism subdivision	1.97e-15	264
multi-cellular organism	6.92e-14	656
subdivision of digestive tract	1.43e-12	118
primordium	7.67e-11	160
trunk	1.03e-10	199
mesenchyme	1.59e-10	160
entire embryonic mesenchyme	1.59e-10	160
organ	2.62e-10	503
anatomical system	3.69e-10	624
anatomical group	5.59e-10	625
immaterial anatomical entity	2.69e-09	117
organ component layer	2.95e-09	66
trunk mesenchyme	3.83e-09	122
orifice	1.23e-08	36
anatomical cluster	2.41e-08	373
respiratory system	2.58e-08	74
reproductive structure	3.91e-08	59
reproductive system	3.91e-08	59
larynx	1.50e-07	9
endo-epithelium	2.03e-07	82
organ part	2.68e-07	218
mouth	2.93e-07	29
stomodeum	2.93e-07	29
integument	4.65e-07	46
integumental system	4.65e-07	46
gut epithelium	5.01e-07	54
foregut	5.16e-07	87
skin of body	6.76e-07	41
anatomical space	8.15e-07	95

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	0.000283677403296032
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0114909503353554
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323553457830301
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.0043539005251408
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320361253918338
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0166841030218175
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00579366600518636
GATA3#2625	2	18.1576775714707	0.00394454681927962	0.0189408977130457
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185711604288785
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00718081516270485
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457047392942257
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00611667948498667
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247329959933115
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00612911116104582
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.0019654557019357
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189483049978367
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00420354241079021

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.