Coexpression cluster:C4534

Full id: C4534_skeletal_squamous_amniotic_heart_left_mesothelioma_somatostatinoma

Phase1 CAGE Peaks

Hg19::chr5:96038476..96038517,+	p1@CAST
Hg19::chr5:96038525..96038547,+	p6@CAST
Hg19::chr5:96038554..96038572,+	p11@CAST

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
organ	1.66e-09	503
endoderm-derived structure	6.59e-08	160
endoderm	6.59e-08	160
presumptive endoderm	6.59e-08	160
multi-cellular organism	3.53e-07	656
digestive system	3.86e-07	145
digestive tract	3.86e-07	145
primitive gut	3.86e-07	145
anatomical system	7.10e-07	624

Disease

Ontology term	p-value	n
cell type cancer	1.35e-07	143

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190923450369849
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.011567019459595
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323963356949663
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322133064540654
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00764590435743445
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00901184782547294
FOSL1#8061	3	39.713579716373	1.59554825631833e-05	0.00037237422199247
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154711792077917
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435773061031529
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.0039310697194772
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109086320174118
JUNB#3726	3	30.6106326598211	3.4847716247536e-05	0.000682057840550303
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157515394837248
MAX#4149	3	6.45255550900712	0.00372191383426551	0.018727739397613
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00722748849606944
MYC#4609	3	5.2222818716094	0.00702084375574015	0.029578455062757
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278012498955033
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203865325666671
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00645078270654426
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191008764605965
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00422742829503869
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330937370286454
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00243662070772004
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109980302354352

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.