Personal tools

Coexpression cluster:C3769

From FANTOM5_SSTAR

Revision as of 16:20, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3769_kidney_ductus_epididymis_seminal_renal_choriocarcinoma_clear



Phase1 CAGE Peaks

Hg19::chr19:20615031..20615039,-p@chr19:20615031..20615039
-
Hg19::chr21:44035172..44035183,-p2@ENST00000419628
p2@uc002zbk.1
Hg19::chr21:44035188..44035208,-p1@ENST00000419628
p1@uc002zbk.1


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
male genital duct4.77e-193
internal male genitalia4.77e-193
duct of male reproductive system2.03e-144
renal system1.54e-1248
urinary bladder6.77e-122
lower urinary tract6.77e-122
cavitated compound organ6.73e-1131
internal genitalia1.19e-1025
urinary system structure1.50e-1047
reproductive organ2.67e-1048
reproductive structure8.07e-1059
reproductive system8.07e-1059
adult organism1.84e-09114
male reproductive organ6.56e-0911
mixed endoderm/mesoderm-derived structure1.35e-0829
kidney9.44e-0826
kidney mesenchyme9.44e-0826
upper urinary tract9.44e-0826
kidney rudiment9.44e-0826
kidney field9.44e-0826
vas deferens1.55e-071
spermatic cord1.55e-071
epididymis1.75e-071
seminal vesicle1.98e-071
seminal fluid secreting gland1.98e-071
epithelium of female gonad2.37e-071
vagina3.40e-071
trunk region element4.38e-07101
intermediate mesoderm6.50e-0728
urinary bladder urothelium9.73e-071
wall of urinary bladder9.73e-071
mucosa of urinary bladder9.73e-071
Disease
Ontology termp-valuen
ovary epithelial cancer2.37e-071
islet cell tumor4.06e-071
endocrine pancreas cancer4.06e-071
pancreatic endocrine carcinoma4.06e-071


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
ESR1#2099220.51240219743630.003099741577095180.0163081915556014
GATA3#2625218.15767757147070.003944546819279620.0189487385703852



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.