Personal tools

Coexpression cluster:C1746

From FANTOM5_SSTAR

Revision as of 15:04, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1746_kidney_renal_Renal_mesothelioma_endometrial_Preadipocyte_Astrocyte



Phase1 CAGE Peaks

Hg19::chr15:66420804..66420837,-p4@MEGF11
Hg19::chr9:133986709..133986719,+p13@AIF1L
Hg19::chr9:133986740..133986750,+p7@AIF1L
Hg19::chr9:133986782..133986794,+p4@AIF1L
Hg19::chr9:133986807..133986821,+p3@AIF1L


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


GO IDGO nameFDR corrected p-value
GO:0016323basolateral plasma membrane0.0200164841634287



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
kidney tubule cell4.32e-6910
nephron tubule epithelial cell4.32e-6910
kidney cell1.90e-4817
kidney epithelial cell1.90e-4817
epithelial cell of nephron1.55e-4515
kidney cortical cell2.96e-2812
renal cortical epithelial cell2.96e-2812
oligodendrocyte4.91e-247
macroglial cell4.91e-247
astrocyte4.91e-247
oligodendrocyte precursor cell4.91e-247
brush border epithelial cell2.30e-223
kidney cortex tubule cell2.30e-223
epithelial cell of proximal tubule2.30e-223
astrocyte of the cerebral cortex4.11e-213
mesangial cell3.61e-152
kidney interstitial cell3.61e-152
juxtaglomerular complex cell3.61e-152
renal interstitial pericyte3.61e-152
extraglomerular mesangial cell3.61e-152
neural cell1.63e-1125
astrocyte of the cerebellum7.13e-103
glial cell (sensu Vertebrata)8.08e-1015
glial cell8.08e-1015
glioblast8.08e-1015
glioblast (sensu Vertebrata)8.08e-1015
neuron associated cell9.15e-0917
neuron associated cell (sensu Vertebrata)9.15e-0917
pericyte cell5.08e-084
serous secreting cell5.82e-081
Uber Anatomy
Ontology termp-valuen
nephron tubule epithelium4.32e-6910
nephron epithelium1.55e-4515
renal tubule1.55e-4515
nephron tubule1.55e-4515
nephron1.55e-4515
uriniferous tubule1.55e-4515
nephrogenic mesenchyme1.55e-4515
kidney9.47e-4426
kidney mesenchyme9.47e-4426
upper urinary tract9.47e-4426
kidney rudiment9.47e-4426
kidney field9.47e-4426
excretory tube1.37e-4216
kidney epithelium1.37e-4216
cavitated compound organ2.66e-3631
cortex of kidney2.96e-2812
renal parenchyma2.96e-2812
urinary system structure4.19e-2347
renal system1.43e-2248
cortex1.89e-2215
parenchyma1.89e-2215
renal cortex tubule2.30e-223
region of nephron tubule2.30e-223
proximal tubule2.30e-223
abdomen element8.70e-2054
abdominal segment element8.70e-2054
abdominal segment of trunk1.47e-1760
abdomen1.47e-1760
compound organ3.36e-1568
abdomen connective tissue3.61e-152
abdominal segment connective tissue3.61e-152
trunk connective tissue3.61e-152
interstitial tissue3.61e-152
extraglomerular mesangium3.61e-152
kidney interstitium3.61e-152
juxtaglomerular apparatus3.61e-152
mesangium3.61e-152
trunk region element2.00e-09101
subdivision of trunk2.93e-08112
stroma5.08e-084
epithelium of female gonad5.82e-081
corpus callosum7.16e-081
central nervous system cell part cluster7.16e-081
axon tract7.16e-081
intercerebral commissure7.16e-081
dorsal telencephalic commissure7.16e-081
brain white matter7.16e-081
brain commissure7.16e-081
white matter7.16e-081
nervous system commissure7.16e-081
cerebral hemisphere white matter7.16e-081
Disease
Ontology termp-valuen
ovary epithelial cancer5.82e-081


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


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.