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Coexpression cluster:C4033: Difference between revisions

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|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322774686214924!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321124938775738!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462958761622385!ELK4#2005;3:16.235681658468:0.000233604395574599:0.00255872149653021!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00763201113328405!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154308245226026!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128259911278574!PRDM1#639;3:131.830955777461:4.35536935195671e-07:2.08178681807326e-05!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277195089893925!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246898141040342!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00154978287494034!STAT2#6773;3:65.2637711864407:3.59360517547754e-06:0.000118469864558617!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000647719353068513
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322774686214924!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321124938775738!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462958761622385!ELK4#2005;3:16.235681658468:0.000233604395574599:0.00255872149653021!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00763201113328405!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154308245226026!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128259911278574!PRDM1#639;3:131.830955777461:4.35536935195671e-07:2.08178681807326e-05!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277195089893925!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246898141040342!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00154978287494034!STAT2#6773;3:65.2637711864407:3.59360517547754e-06:0.000118469864558617!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000647719353068513
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}}
}}

Revision as of 16:30, 26 November 2012


Full id: C4033_Bronchial_bile_renal_signet_Keratinocyte_hepatoma_squamous



Phase1 CAGE Peaks

Hg19::chr20:388993..389028,+p3@RBCK1
Hg19::chr20:389045..389056,+p6@RBCK1
Hg19::chr20:389126..389137,+p5@RBCK1


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><br>


Cell Type
Ontology termp-valuen
epithelial cell6.42e-14253
animal cell8.21e-14679
eukaryotic cell8.21e-14679
embryonic cell5.85e-13250
somatic cell2.11e-12588
endodermal cell1.05e-1158
native cell7.94e-11722
endo-epithelial cell8.50e-1042
squamous epithelial cell1.43e-0763
mesodermal cell5.22e-07121
Uber Anatomy
Ontology termp-valuen
epithelial tube2.75e-10117
unilaminar epithelium4.63e-10148
endo-epithelium4.74e-0982
trunk1.14e-08199
organism subdivision4.16e-08264
gut epithelium1.06e-0754
mesenchyme1.31e-07160
entire embryonic mesenchyme1.31e-07160
artery1.70e-0742
arterial blood vessel1.70e-0742
arterial system1.70e-0742
trunk mesenchyme3.06e-07122
endoderm-derived structure4.62e-07160
endoderm4.62e-07160
presumptive endoderm4.62e-07160


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
E2F6#187635.017155731697390.00791769806886330.0322774686214924
EGR1#195834.988179094810140.008056488137383440.0321124938775738
ELF1#199734.258097958807540.01295179875054610.0462958761622385
ELK4#2005316.2356816584680.0002336043955745990.00255872149653021
ETS1#211339.728760922202340.001085840092584840.00763201113328405
GABPB1#255337.067683836182170.002832212825417420.0154308245226026
IRF1#365937.63716375356390.002244692747297240.0128259911278574
PRDM1#6393131.8309557774614.35536935195671e-072.08178681807326e-05
SIN3A#2594235.408884726815140.006318961977991520.0277195089893925
SP1#666735.69838137814090.005403962701712170.0246898141040342
STAT1#6772320.70658749719920.0001125992441046670.00154978287494034
STAT2#6773365.26377118644073.59360517547754e-060.000118469864558617
THAP1#55145331.36914460285133.23800758564397e-050.000647719353068513



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.