Coexpression cluster:C4040

Full id: C4040_testicular_granulocyte_hepatoblastoma_somatostatinoma_smallcell_tubular_extraskeletal

Phase1 CAGE Peaks

Hg19::chr20:43538692..43538742,+	p1@PABPC1L
Hg19::chr20:43538744..43538755,+	p3@PABPC1L
Hg19::chr20:43538756..43538769,+	p2@PABPC1L

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
digestive system	1.58e-08	155
digestive tract	1.58e-08	155
primitive gut	1.58e-08	155
endoderm-derived structure	7.37e-08	169
endoderm	7.37e-08	169
presumptive endoderm	7.37e-08	169
gastrointestinal system	7.91e-08	35
endo-epithelium	1.13e-07	82
subdivision of digestive tract	1.37e-07	129
endodermal part of digestive tract	1.37e-07	129
endocrine system	2.62e-07	45

Disease

Ontology term	p-value	n
cancer	6.95e-37	235
disease of cellular proliferation	3.73e-36	239
cell type cancer	5.68e-32	143
carcinoma	3.86e-22	106
organ system cancer	1.87e-15	137
germ cell and embryonal cancer	1.79e-09	22
germ cell cancer	1.79e-09	22
disease of anatomical entity	5.07e-09	39

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	0.0190303913862993
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325892254722602
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322812487747507
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321137194984997
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463006301457567
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00243312523658476
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154324346675938
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.010884374026268
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128273947162933
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294927962756715
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173121100587888
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277218377728075
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203358258055751
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00375551735008073
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00629947131983395
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000647843437235768
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140419580973561
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00243006477756474

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.