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Coexpression cluster:C1933: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!3.65e-13!169;UBERON:0000925!3.65e-13!169;UBERON:0006595!3.65e-13!169;UBERON:0000481!1.72e-12!347;UBERON:0001007!2.04e-12!155;UBERON:0001555!2.04e-12!155;UBERON:0007026!2.04e-12!155;UBERON:0000468!3.18e-09!659;UBERON:0003104!4.22e-09!238;UBERON:0009142!4.22e-09!238;UBERON:0000475!2.27e-08!365;UBERON:0001046!1.31e-07!19;UBERON:0004921!1.63e-07!129;UBERON:0004185!1.63e-07!129;UBERON:0005156!1.71e-07!59;UBERON:0000990!1.71e-07!59;UBERON:0000161!3.04e-07!35;UBERON:0002100!3.47e-07!216;UBERON:0005256!4.51e-07!143;UBERON:0000077!7.07e-07!130
|ontology_enrichment_uberon=UBERON:0004119!3.65e-13!169;UBERON:0000925!3.65e-13!169;UBERON:0006595!3.65e-13!169;UBERON:0000481!1.72e-12!347;UBERON:0001007!2.04e-12!155;UBERON:0001555!2.04e-12!155;UBERON:0007026!2.04e-12!155;UBERON:0000468!3.18e-09!659;UBERON:0003104!4.22e-09!238;UBERON:0009142!4.22e-09!238;UBERON:0000475!2.27e-08!365;UBERON:0001046!1.31e-07!19;UBERON:0004921!1.63e-07!129;UBERON:0004185!1.63e-07!129;UBERON:0005156!1.71e-07!59;UBERON:0000990!1.71e-07!59;UBERON:0000161!3.04e-07!35;UBERON:0002100!3.47e-07!216;UBERON:0005256!4.51e-07!143;UBERON:0000077!7.07e-07!130
|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00250113171896469!CTCFL#140690;4:15.7971794871795:3.15350622350688e-05:0.000633729144654291!E2F1#1869;5:4.90738921487932:0.000351281809925646:0.0035341027788098!E2F6#1876;5:5.01715573169739:0.000314497859929779:0.00323158618587231!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.0057367290838526!EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110961740073157!GABPB1#2553;5:7.06768383618217:5.6685482528729e-05:0.0009492023584765!NANOG#79923;5:29.2447784810127:4.66760911383881e-08:3.0448496454729e-06!RAD21#5885;5:10.3550338954563:8.39503550283973e-06:0.000229761297924811!SMC3#9126;5:15.0449328449328:1.29633924985553e-06:5.16552365187569e-05!SP1#6667;5:5.6983813781409:0.00016639184371255:0.00204492795545952!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135513215329398!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00920074945066268!TCF12#6938;5:10.6344649021864:7.34844389925727e-06:0.000211422626004003!YY1#7528;5:4.91117074985386:0.0003499314082136:0.00353037928346408!ZEB1#6935;5:16.8884320175439:7.27243686732534e-07:3.23477867967032e-05!ZNF143#7702;5:13.5008765522279:2.22790360787208e-06:7.97668923217524e-05
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}}
}}

Revision as of 12:43, 5 September 2012


Full id: C1933_glioblastoma_small_Prostate_Smooth_rhabdomyosarcoma_normal_sacrococcigeal



Phase1 CAGE Peaks

Hg19::chr4:120549834..120549846,-p15@PDE5A
Hg19::chr4:120549851..120549880,-p1@PDE5A
Hg19::chr4:120549895..120549908,-p12@PDE5A
Hg19::chr4:120549931..120549938,-p21@PDE5A
Hg19::chr4:120549947..120549969,-p2@PDE5A


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
non-terminally differentiated cell2.92e-11180
fibroblast1.51e-0875


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
CTCF#1066455.360256373075030.0002259278299937090.00250113171896469
CTCFL#140690415.79717948717953.15350622350688e-050.000633729144654291
E2F1#186954.907389214879320.0003512818099256460.0035341027788098
E2F6#187655.017155731697390.0003144978599297790.00323158618587231
ELF1#199754.258097958807540.0007142416939776840.0057367290838526
EP300#203356.77394172622327.00901578206049e-050.00110961740073157
GABPB1#255357.067683836182175.6685482528729e-050.0009492023584765
NANOG#79923529.24477848101274.66760911383881e-083.0448496454729e-06
RAD21#5885510.35503389545638.39503550283973e-060.000229761297924811
SMC3#9126515.04493284493281.29633924985553e-065.16552365187569e-05
SP1#666755.69838137814090.000166391843712550.00204492795545952
TAF1#687253.343046285745290.002394600090870310.0135513215329398
TBP#690853.706770687096390.001428755106721120.00920074945066268
TCF12#6938510.63446490218647.34844389925727e-060.000211422626004003
YY1#752854.911170749853860.00034993140821360.00353037928346408
ZEB1#6935516.88843201754397.27243686732534e-073.23477867967032e-05
ZNF143#7702513.50087655222792.22790360787208e-067.97668923217524e-05



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.