Personal tools

Coexpression cluster:C2474

From FANTOM5_SSTAR

Revision as of 15:12, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2474_mesothelioma_Hep2_clear_Renal_nonsmall_renal_lung



Phase1 CAGE Peaks

Hg19::chr19:10687983..10687998,-p@chr19:10687983..10687998
-
Hg19::chr19:10688000..10688029,-p@chr19:10688000..10688029
-
Hg19::chr19:10688031..10688042,-p@chr19:10688031..10688042
-
Hg19::chr19:10688044..10688070,-p@chr19:10688044..10688070
-


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
epithelial cell1.17e-18254
mesothelial cell7.07e-1719
kidney cell4.64e-1018
kidney epithelial cell4.64e-1018
epithelial cell of nephron1.63e-0816
kidney tubule cell8.61e-0812
nephron tubule epithelial cell8.61e-0812
Uber Anatomy
Ontology termp-valuen
abdomen element1.01e-1255
abdominal segment element1.01e-1255
abdominal segment of trunk2.37e-1261
abdomen2.37e-1261
larynx2.94e-109
subdivision of trunk3.72e-09113
kidney6.63e-0927
kidney mesenchyme6.63e-0927
kidney rudiment6.63e-0927
kidney field6.63e-0927
nephron epithelium1.63e-0816
nephron1.63e-0816
uriniferous tubule1.63e-0816
metanephric mesenchyme1.63e-0816
nephrogenic mesenchyme1.63e-0816
cortex1.90e-0816
renal tubule8.61e-0812
nephron tubule8.61e-0812
nephron tubule epithelium8.61e-0812
excretory tube9.96e-0817
mesonephric epithelium9.96e-0817
mesonephric tubule9.96e-0817
nephric duct9.96e-0817
kidney epithelium9.96e-0817
renal duct9.96e-0817
mesonephric duct9.96e-0817
pronephric duct9.96e-0817
immaterial anatomical entity2.41e-07126
body cavity precursor4.19e-0763
mesonephros4.89e-0718
pronephros4.89e-0718
nephrogenic cord4.89e-0718
pronephric mesoderm4.89e-0718
rostral part of nephrogenic cord4.89e-0718
presumptive pronephric mesoderm4.89e-0718
urogenital ridge6.40e-0720
trunk region element8.73e-07107
Disease
Ontology termp-valuen
carcinoma1.02e-17106
disease of cellular proliferation1.49e-16239
cell type cancer6.52e-16143
cancer1.22e-14235
reproductive organ cancer6.17e-1029
female reproductive organ cancer8.57e-0927
ovarian cancer4.50e-0814


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
EGR1#195844.988179094810140.001615011500076050.0101431346476904
FOXA1#3169411.08141974938556.62943068949433e-050.00107095299579288
FOXA2#3170424.63046375266522.71504128667089e-069.43300721685365e-05
HDAC2#3066413.41562023662633.0859005065161e-050.000626654409877571
HEY1#2346244.040111043105710.00375304636917980.0186038449736945
JUN#3725412.51282919233634.07770316866756e-050.000743360518820861
JUND#372746.994663941871030.000417684217818580.00391725233699306
MAFK#7975427.10073313782991.85228494563408e-066.85024034833846e-05
TAF1#687243.343046285745290.008005664898701650.0322210349668774
TBP#690843.706770687096390.005296377814784350.0244204848615188



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.