Coexpression cluster:C3639

Full id: C3639_testis_testicular_small_epidermoid_choriocarcinoma_argyrophil_hereditary

Phase1 CAGE Peaks

Hg19::chr17:42733789..42733802,+	p3@C17orf104
Hg19::chr17:42733803..42733843,+	p1@C17orf104
Hg19::chr7:99775520..99775578,+	p1@STAG3

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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GO ID	GO name	FDR corrected p-value
GO:0007130	synaptonemal complex assembly	0.00360591075002944
GO:0007129	synapsis	0.00360591075002944
GO:0000795	synaptonemal complex	0.00446446092860787
GO:0000794	condensed nuclear chromosome	0.00664986138317117
GO:0007127	meiosis I	0.00664986138317117
GO:0000793	condensed chromosome	0.00664986138317117
GO:0007059	chromosome segregation	0.00664986138317117
GO:0044454	nuclear chromosome part	0.00664986138317117
GO:0051327	M phase of meiotic cell cycle	0.00664986138317117
GO:0007126	meiosis	0.00664986138317117
GO:0051321	meiotic cell cycle	0.00664986138317117
GO:0000228	nuclear chromosome	0.00849964676792652
GO:0000279	M phase	0.0242507404287694
GO:0022403	cell cycle phase	0.0271547156481808
GO:0044427	chromosomal part	0.0318693826288316
GO:0005694	chromosome	0.0324834985212736
GO:0051276	chromosome organization and biogenesis	0.0324834985212736
GO:0022402	cell cycle process	0.0357729241074349
GO:0022607	cellular component assembly	0.0432194159896385
GO:0007049	cell cycle	0.0432194159896385

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
germ line cell	5.02e-13	7
germ cell	5.02e-13	7
embryonic stem cell	1.10e-11	5

Uber Anatomy

Ontology term	p-value	n
testis	1.78e-11	8
male reproductive organ	1.62e-10	11

Disease

Ontology term	p-value	n
bronchus cancer	6.34e-09	7
bronchogenic carcinoma	6.34e-09	7
respiratory system cancer	1.44e-08	16
cell type cancer	2.70e-08	143
lung cancer	3.89e-07	15
cancer	5.38e-07	235

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)
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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
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186325835939438
SETDB1#9869	3	40.3200261780105	1.52461559299059e-05	0.000358382462111961

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.