Personal tools

Coexpression cluster:C4148

From FANTOM5_SSTAR

Revision as of 15:43, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


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>


Cell Type
Ontology termp-valuen
skin fibroblast1.68e-1223
kidney tubule cell3.63e-1010
nephron tubule epithelial cell3.63e-1010
kidney cell1.07e-0917
kidney epithelial cell1.07e-0917
epithelial cell of nephron1.69e-0915
Uber Anatomy
Ontology termp-valuen
urinary system structure9.47e-2047
renal system3.94e-1948
cavitated compound organ9.35e-1531
kidney2.30e-1326
kidney mesenchyme2.30e-1326
upper urinary tract2.30e-1326
kidney rudiment2.30e-1326
kidney field2.30e-1326
excretory tube2.71e-1016
kidney epithelium2.71e-1016
nephron tubule epithelium3.63e-1010
nephron epithelium1.69e-0915
renal tubule1.69e-0915
nephron tubule1.69e-0915
nephron1.69e-0915
uriniferous tubule1.69e-0915
nephrogenic mesenchyme1.69e-0915
intermediate mesoderm5.59e-0928
reproductive structure8.98e-0959
reproductive system8.98e-0959
large intestine3.53e-0811
colon3.61e-089
abdomen element4.18e-0754
abdominal segment element4.18e-0754
Disease
Ontology termp-valuen
squamous cell carcinoma5.31e-0914
musculoskeletal system disease2.74e-085
myotonic disease2.74e-085
muscle tissue disease2.74e-085
myopathy2.74e-085
muscular disease2.74e-085
myotonic dystrophy2.74e-085
cell type cancer1.87e-07143


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.