Coexpression cluster:C4305

Full id: C4305_epidermoid_papillotubular_mesothelioma_malignant_bronchioalveolar_myxofibrosarcoma_gall

Phase1 CAGE Peaks

Hg19::chr3:170626612..170626637,+	p@chr3:170626612..170626637 +
Hg19::chr3:170626640..170626659,+	p@chr3:170626640..170626659 +
Hg19::chr3:170626681..170626687,+	p@chr3:170626681..170626687 +

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
mesothelial cell	2.82e-15	19
squamous epithelial cell	3.96e-10	63
epithelial cell	1.72e-08	253
germ line cell	3.39e-08	7
germ cell	3.39e-08	7

Uber Anatomy

Ontology term	p-value	n
body cavity	3.63e-07	46
testis	3.84e-07	8

Disease

Ontology term	p-value	n
cancer	1.73e-28	235
disease of cellular proliferation	2.21e-27	239
cell type cancer	2.30e-23	143
carcinoma	9.01e-20	106
squamous cell carcinoma	1.26e-10	14
organ system cancer	5.87e-08	137
germ cell and embryonal cancer	7.81e-08	22
germ cell cancer	7.81e-08	22
respiratory system cancer	2.73e-07	16

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
ATF3#467	3	22.4631745260087	8.81932387510763e-05	0.00129912745584255
BHLHE40#8553	3	44.8718135469774	1.10603738662898e-05	0.000285218366968257
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190622029617965
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326627060205639
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323418518700725
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321652801934397
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463831879336242
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00256140781831134
FOS#2353	3	8.9979553088944	0.00137249927241713	0.0089994005218466
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154550120316511
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128463732716848
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157207034371336
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187070099108165
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00721761217945825
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295379431600768
NFE2#4778	3	77.204260651629	2.17039522930409e-06	7.83796360142774e-05
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00200081124790942
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.0024638066467355
REST#5978	3	9.65002871612802	0.00111263624711459	0.00769757664364074
SETDB1#9869	3	40.3200261780105	1.52461559299059e-05	0.000359596494842693
SIRT6#51548	3	153.638403990025	2.75057764221434e-07	1.40198915751695e-05
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247287587347902
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00615904687660031
USF1#7391	3	6.36149927720796	0.0038840405729056	0.019085598635254
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00422480256317842
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330441212310012
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140607408128421

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.