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Coexpression cluster:C3635: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189837504270635!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320232755311204!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00761458762032282!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.0058081370147361!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127930949978159!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00199387975511413!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00245562305512766!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276336182069951!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00612968797025102
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189837504270635!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320232755311204!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00761458762032282!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.0058081370147361!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127930949978159!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00199387975511413!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00245562305512766!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276336182069951!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00612968797025102
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}}
}}

Revision as of 16:15, 26 November 2012


Full id: C3635_testicular_hepatoblastoma_hepatocellular_lung_gastric_prostate_Trabecular



Phase1 CAGE Peaks

Hg19::chr17:41623667..41623682,-p8@ETV4
Hg19::chr17:41623692..41623715,-p1@ETV4
Hg19::chr17:41623716..41623727,-p12@ETV4


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 cell1.72e-32253
embryonic cell2.33e-24250
animal cell1.28e-14679
eukaryotic cell1.28e-14679
endodermal cell4.01e-1058
endo-epithelial cell1.35e-0842
ectodermal cell2.03e-0772
squamous epithelial cell3.90e-0763
mesodermal cell8.47e-07121
meso-epithelial cell9.99e-0745
Uber Anatomy
Ontology termp-valuen
epithelial tube8.53e-10117
organism subdivision1.38e-09264
unilaminar epithelium3.24e-09148
cell layer1.45e-08309
epithelium7.62e-08306
anatomical cluster1.14e-07373
Disease
Ontology termp-valuen
cancer7.89e-13235
disease of cellular proliferation4.61e-12239
carcinoma9.80e-11106
cell type cancer1.37e-10143


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
CCNT2#90536.336201576962630.003930750035764890.0189837504270635
EGR1#195834.988179094810140.008056488137383440.0320232755311204
ETS1#211339.728760922202340.001085840092584840.00761458762032282
FOXA1#3169311.08141974938550.000734755275698670.0058081370147361
IRF1#365937.63716375356390.002244692747297240.0127930949978159
NFYA#4800318.42558069983050.0001598135507814160.00199387975511413
NFYB#4801316.75979325353650.0002123649923296180.00245562305512766
SIN3A#2594235.408884726815140.006318961977991520.0276336182069951
TCF7L2#6934310.77017656313730.0008003181298398380.00612968797025102



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.