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Coexpression cluster:C4148

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Full id: C4148_neuroectodermal_Fibroblast_neuroblastoma_glioblastoma_tridermal_rhabdomyosarcoma_kidney



Phase1 CAGE Peaks

Hg19::chr2:176969097..176969109,+p3@HOXD11
Hg19::chr2:176969124..176969155,+p5@HOXD11
Hg19::chr2:176970198..176970230,+p@chr2:176970198..176970230
+


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
renal system3.06e-1945
urinary system structure1.21e-1844
intermediate mesoderm2.18e-1437
cavitated compound organ4.73e-1432
kidney3.31e-1327
kidney mesenchyme3.31e-1327
kidney rudiment3.31e-1327
kidney field3.31e-1327
urogenital ridge5.40e-1120
mesonephros7.25e-1118
pronephros7.25e-1118
nephrogenic cord7.25e-1118
pronephric mesoderm7.25e-1118
rostral part of nephrogenic cord7.25e-1118
presumptive pronephric mesoderm7.25e-1118
excretory tube4.41e-1017
mesonephric epithelium4.41e-1017
mesonephric tubule4.41e-1017
nephric duct4.41e-1017
kidney epithelium4.41e-1017
renal duct4.41e-1017
mesonephric duct4.41e-1017
pronephric duct4.41e-1017
renal tubule1.71e-0912
nephron tubule1.71e-0912
nephron tubule epithelium1.71e-0912
nephron epithelium1.88e-0916
nephron1.88e-0916
uriniferous tubule1.88e-0916
metanephric mesenchyme1.88e-0916
nephrogenic mesenchyme1.88e-0916
intraembryonic coelom1.19e-0821
reproductive structure1.73e-0859
reproductive system1.73e-0859
large intestine3.58e-0811
hindgut8.11e-0819
body cavity precursor2.62e-0763
duct4.76e-0726
cortex of kidney5.17e-0713
renal parenchyma5.17e-0713
colon7.82e-079
Disease
Ontology termp-valuen
cell type cancer1.91e-07143
squamous cell carcinoma3.49e-0714
musculoskeletal system disease6.28e-075
myotonic disease6.28e-075
muscle tissue disease6.28e-075
myopathy6.28e-075
muscular disease6.28e-075
myotonic dystrophy6.28e-075


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)

{{{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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
SUZ12#23512233.41052060737530.00117826764536030.00800111148334096
TRIM28#10155212.39368336350830.008368344129438470.0329257644866796



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.