Personal tools

Coexpression cluster:C4533

From FANTOM5_SSTAR

Revision as of 16:48, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4533_lung_gall_rectal_salivary_Prostate_Keratinocyte_amniotic



Phase1 CAGE Peaks

Hg19::chr5:95998673..95998713,+p7@CAST
Hg19::chr5:95998714..95998744,+p5@CAST
Hg19::chr5:95998746..95998764,+p12@CAST


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
endo-epithelial cell6.26e-1542
endodermal cell5.84e-1358
epithelial cell7.77e-12253
epithelial cell of alimentary canal2.26e-0720
vascular associated smooth muscle cell3.59e-0732
embryonic cell8.55e-07250
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure9.38e-19160
endoderm9.38e-19160
presumptive endoderm9.38e-19160
digestive system7.25e-16145
digestive tract7.25e-16145
primitive gut7.25e-16145
organism subdivision8.46e-14264
subdivision of digestive tract1.30e-12118
respiratory system4.15e-1274
surface structure1.80e-1099
trunk1.09e-09199
orifice3.89e-0936
respiratory tract6.72e-0954
female organism1.29e-0841
anatomical system2.30e-08624
multi-cellular organism3.35e-08656
anatomical group3.44e-08625
multi-tissue structure8.69e-08342
respiratory primordium1.14e-0738
endoderm of foregut1.14e-0738
multilaminar epithelium1.70e-0783
segment of respiratory tract2.90e-0747
female reproductive organ6.09e-0737
female reproductive system6.09e-0737
artery7.01e-0742
arterial blood vessel7.01e-0742
arterial system7.01e-0742
Disease
Ontology termp-valuen
carcinoma3.01e-08106


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
E2F1#186934.907389214879320.008460985347239390.032728031432605
EBF1#187938.9064668465690.00141523283560980.00918502996012008
ELF1#199734.258097958807540.01295179875054610.0464548701733733
GTF2F1#2962312.73966087675770.0004835525047438590.00435735461975357
JUND#372736.994663941871030.002921845042734990.0157507264590792
NRF1#4899312.21027944771090.0005492172401020010.00473030672431246
PBX3#5090321.91451268674419.49854535978121e-050.0013730360952667
SMARCB1#6598318.25271578115740.000164397760679890.00203841122256287
SRF#6722313.79717826216780.0003806615025800190.00376155801570202
TFAP2A#7020316.5186343730450.0002218033880766340.00249272829520452
TFAP2C#7022310.80922860986020.0007916746575753130.00618319694604458



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.