Coexpression cluster:C3768

Full id: C3768_testicular_H9_iPS_Hodgkin_migratory_acute_Neural

Phase1 CAGE Peaks

Hg19::chr19:20011731..20011743,+	p3@ZNF93
Hg19::chr19:20011744..20011770,+	p1@ZNF93
Hg19::chr19:20011775..20011800,+	p2@ZNF93

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><br>disease_data<br>

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Cell Type

Ontology term	p-value	n
neural cell	2.11e-09	25
neurectodermal cell	1.70e-07	59

Disease

Ontology term	p-value	n
myeloid leukemia	1.19e-07	31

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
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00660277632773309
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00437020033141206
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322133412003901
FOS#2353	3	8.9979553088944	0.00137249927241713	0.0089723617621415
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00433789211844562
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186450958814685
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199530991393429
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00245725542143951
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00136604045556347
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246413054752059
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000939729372187272
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109052215749046
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00542776288365137
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190220545553898
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00421545151722185
YY1#7528	3	4.91117074985386	0.00844145534180826	0.032930567549795

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.