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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0001008!4.99e-19!45;UBERON:0006554!1.20e-18!44;UBERON:0000489!7.46e-14!32;UBERON:0002113!1.90e-12!27;UBERON:0003918!1.90e-12!27;UBERON:0005095!1.90e-12!27;UBERON:0007687!1.90e-12!27;UBERON:0003064!1.19e-10!37;UBERON:0000080!4.22e-09!18;UBERON:0002120!4.22e-09!18;UBERON:0004875!4.22e-09!18;UBERON:0005721!4.22e-09!18;UBERON:0005754!4.22e-09!18;UBERON:0007297!4.22e-09!18;UBERON:0006555!5.40e-09!17;UBERON:0005103!5.40e-09!17;UBERON:0000083!5.40e-09!17;UBERON:0009201!5.40e-09!17;UBERON:0004819!5.40e-09!17;UBERON:0006553!5.40e-09!17;UBERON:0003074!5.40e-09!17;UBERON:0003060!5.40e-09!17;UBERON:0004876!1.33e-08!20;UBERON:0004211!1.46e-08!16;UBERON:0001285!1.46e-08!16;UBERON:0007684!1.46e-08!16;UBERON:0003220!1.46e-08!16;UBERON:0004208!1.46e-08!16;UBERON:0009773!3.00e-08!12;UBERON:0001231!3.00e-08!12;UBERON:0004810!3.00e-08!12;UBERON:0003887!3.97e-08!21
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}}
}}

Revision as of 20:14, 8 August 2012


Full id: C4681_smallcell_acute_small_clear_renal_endometrioid_embryonic



Phase1 CAGE Peaks

Hg19::chr7:27205089..27205096,-p4@HOXA9
Hg19::chr7:27205106..27205134,-p2@HOXA9
Hg19::chr7:27205136..27205164,-p1@HOXA9


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

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

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><br>

Cell Type
Ontology termp-valuen
kidney cell6.51e-1018
kidney epithelial cell6.51e-1018
epithelial cell of nephron1.46e-0816
kidney tubule cell3.00e-0812
nephron tubule epithelial cell3.00e-0812
Uber Anatomy
Ontology termp-valuen
renal system4.99e-1945
urinary system structure1.20e-1844
cavitated compound organ7.46e-1432
kidney1.90e-1227
kidney mesenchyme1.90e-1227
kidney rudiment1.90e-1227
kidney field1.90e-1227
intermediate mesoderm1.19e-1037
mesonephros4.22e-0918
pronephros4.22e-0918
nephrogenic cord4.22e-0918
pronephric mesoderm4.22e-0918
rostral part of nephrogenic cord4.22e-0918
presumptive pronephric mesoderm4.22e-0918
excretory tube5.40e-0917
mesonephric epithelium5.40e-0917
mesonephric tubule5.40e-0917
nephric duct5.40e-0917
kidney epithelium5.40e-0917
renal duct5.40e-0917
mesonephric duct5.40e-0917
pronephric duct5.40e-0917
urogenital ridge1.33e-0820
nephron epithelium1.46e-0816
nephron1.46e-0816
uriniferous tubule1.46e-0816
metanephric mesenchyme1.46e-0816
nephrogenic mesenchyme1.46e-0816
renal tubule3.00e-0812
nephron tubule3.00e-0812
nephron tubule epithelium3.00e-0812
intraembryonic coelom3.97e-0821


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

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

No analysis results for this cluster

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

This analysis result is provided for C0 - C305 clusters.

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