Coexpression cluster:C4317

Full id: C4317_renal_squamous_bile_glassy_epidermoid_epithelioid_malignant

Phase1 CAGE Peaks

Hg19::chr3:194040528..194040540,-	p@chr3:194040528..194040540 -
Hg19::chr3:194040578..194040593,-	p@chr3:194040578..194040593 -
Hg19::chr3:194040598..194040638,-	p@chr3:194040598..194040638 -

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	5.07e-39	253
endo-epithelial cell	9.93e-15	42
endodermal cell	3.07e-14	58
epithelial cell of alimentary canal	2.26e-11	20
squamous epithelial cell	8.08e-09	63

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	6.18e-18	160
endoderm	6.18e-18	160
presumptive endoderm	6.18e-18	160
digestive system	1.11e-16	145
digestive tract	1.11e-16	145
primitive gut	1.11e-16	145
larynx	1.98e-14	9
subdivision of digestive tract	3.71e-14	118
foregut	1.62e-13	87
upper respiratory tract	7.23e-12	19
respiratory system	1.16e-10	74
segment of respiratory tract	1.43e-10	47
respiratory tract	2.70e-10	54
respiratory primordium	2.96e-09	38
endoderm of foregut	2.96e-09	38
biliary system	1.42e-08	9
biliary tree	1.42e-08	9
biliary bud	1.42e-08	9
orifice	2.36e-07	36
viscus	8.18e-07	18

Disease

Ontology term	p-value	n
carcinoma	3.28e-50	106
cell type cancer	5.02e-37	143
cancer	3.06e-25	235
disease of cellular proliferation	3.26e-24	239
adenocarcinoma	1.75e-17	25
squamous cell carcinoma	6.35e-16	14

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
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115547030860391
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.03266632836791
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167967094565713
ESR1#2099	3	30.7686032961545	3.43136389821584e-05	0.000678470681873843
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00899996556237663
FOSL1#8061	3	39.713579716373	1.59554825631833e-05	0.000371875617812163
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00243615562354156
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00388784961137772
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435059786724189
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00445378967231835
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157223233766912
MAX#4149	3	6.45255550900712	0.00372191383426551	0.018709711154065
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00721859859632028
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295427035054692
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00309598817199873
SMARCC1#6599	3	43.6633593196315	1.20046018043203e-05	0.000302108098275038
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00310024945478481
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.0064438319314133
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.0024895135999286
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00617534614702428
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00197597127232543

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.