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Coexpression cluster:C1534: Difference between revisions

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|tf_chipseq_enrich=BHLHE40#8553;6:44.8718135469774:1.22070649245094e-10:1.31161898523748e-08!CTCF#10664;6:5.36025637307503:4.21437267579784e-05:0.000756262659600774!E2F1#1869;6:4.90738921487932:7.15746523583771e-05:0.00112798930400733!E2F6#1876;6:5.01715573169739:6.26776799983417e-05:0.00102521444343724!EGR1#1958;6:4.98817909481014:6.48943962979974e-05:0.00105552185873953!EP300#2033;6:6.7739417262232:1.03454107484288e-05:0.000270048576144752!FOS#2353;6:8.9979553088944:1.88302066097805e-06:6.94669003221076e-05!JUND#3727;6:6.99466394187103:8.53468650061654e-06:0.00023242610780649!MAX#4149;6:6.45255550900712:1.3848964723355e-05:0.000334730855529386!MXI1#4601;6:9.9615716287593:1.02262624227062e-06:4.3047989567312e-05!MYC#4609;6:5.2222818716094:4.92821127172503e-05:0.00085469521256674!NR3C1#2908;6:14.973023331173:8.86442195171695e-08:5.24825036403269e-06!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380744956256576!RAD21#5885;6:10.3550338954563:8.10515055094479e-07:3.54626652027701e-05!SMC3#9126;6:15.0449328449328:8.61317699636729e-08:5.12857236216421e-06!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.00573827594210693!TCF7L2#6934;6:10.7701765631373:6.40204410218762e-07:2.91593146091745e-05!TFAP2A#7020;6:16.518634373045:4.91595718330683e-08:3.16143874548881e-06!TFAP2C#7022;6:10.8092286098602:6.2644941908553e-07:2.8670355337368e-05!USF1#7391;6:6.36149927720796:1.50818327938273e-05:0.000357091710531519!USF2#7392;6:12.9921973850696:2.07721573629339e-07:1.11423900504748e-05
|tf_chipseq_enrich=BHLHE40#8553;6:44.8718135469774:1.22070649245094e-10:1.31161898523748e-08!CTCF#10664;6:5.36025637307503:4.21437267579784e-05:0.000756262659600774!E2F1#1869;6:4.90738921487932:7.15746523583771e-05:0.00112798930400733!E2F6#1876;6:5.01715573169739:6.26776799983417e-05:0.00102521444343724!EGR1#1958;6:4.98817909481014:6.48943962979974e-05:0.00105552185873953!EP300#2033;6:6.7739417262232:1.03454107484288e-05:0.000270048576144752!FOS#2353;6:8.9979553088944:1.88302066097805e-06:6.94669003221076e-05!JUND#3727;6:6.99466394187103:8.53468650061654e-06:0.00023242610780649!MAX#4149;6:6.45255550900712:1.3848964723355e-05:0.000334730855529386!MXI1#4601;6:9.9615716287593:1.02262624227062e-06:4.3047989567312e-05!MYC#4609;6:5.2222818716094:4.92821127172503e-05:0.00085469521256674!NR3C1#2908;6:14.973023331173:8.86442195171695e-08:5.24825036403269e-06!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380744956256576!RAD21#5885;6:10.3550338954563:8.10515055094479e-07:3.54626652027701e-05!SMC3#9126;6:15.0449328449328:8.61317699636729e-08:5.12857236216421e-06!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.00573827594210693!TCF7L2#6934;6:10.7701765631373:6.40204410218762e-07:2.91593146091745e-05!TFAP2A#7020;6:16.518634373045:4.91595718330683e-08:3.16143874548881e-06!TFAP2C#7022;6:10.8092286098602:6.2644941908553e-07:2.8670355337368e-05!USF1#7391;6:6.36149927720796:1.50818327938273e-05:0.000357091710531519!USF2#7392;6:12.9921973850696:2.07721573629339e-07:1.11423900504748e-05
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}}
}}

Revision as of 14:57, 26 November 2012


Full id: C1534_gastric_signet_endometrial_pharyngeal_papillotubular_bile_squamous



Phase1 CAGE Peaks

Hg19::chr7:116312178..116312192,+p7@MET
Hg19::chr7:116312193..116312211,+p5@MET
Hg19::chr7:116312213..116312230,+p3@MET
Hg19::chr7:116312243..116312256,+p2@MET
Hg19::chr7:116312277..116312288,+p8@MET
Hg19::chr7:116312308..116312319,+p9@MET


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 cell9.18e-38253
endo-epithelial cell1.34e-1242
endodermal cell7.58e-1258
embryonic cell1.90e-09250
squamous epithelial cell6.19e-0863
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.08e-14160
endoderm2.08e-14160
presumptive endoderm2.08e-14160
digestive system1.81e-11145
digestive tract1.81e-11145
primitive gut1.81e-11145
subdivision of digestive tract1.22e-10118
anatomical system1.96e-10624
anatomical group2.58e-10625
multi-cellular organism1.15e-09656
organ2.77e-09503
respiratory primordium4.16e-0938
endoderm of foregut4.16e-0938
organ part5.13e-09218
trunk region element6.22e-09101
respiratory tract3.00e-0854
renal system3.28e-0848
urinary system structure5.71e-0847
endo-epithelium6.06e-0882
respiratory system8.00e-0874
multi-tissue structure1.18e-07342
anatomical cluster1.36e-07373
foregut4.79e-0787
epithelial bud8.10e-0737
organism subdivision9.27e-07264
Disease
Ontology termp-valuen
carcinoma5.40e-18106
cell type cancer7.11e-17143
adenocarcinoma2.85e-0725


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
BHLHE40#8553644.87181354697741.22070649245094e-101.31161898523748e-08
CTCF#1066465.360256373075034.21437267579784e-050.000756262659600774
E2F1#186964.907389214879327.15746523583771e-050.00112798930400733
E2F6#187665.017155731697396.26776799983417e-050.00102521444343724
EGR1#195864.988179094810146.48943962979974e-050.00105552185873953
EP300#203366.77394172622321.03454107484288e-050.000270048576144752
FOS#235368.99795530889441.88302066097805e-066.94669003221076e-05
JUND#372766.994663941871038.53468650061654e-060.00023242610780649
MAX#414966.452555509007121.3848964723355e-050.000334730855529386
MXI1#460169.96157162875931.02262624227062e-064.3047989567312e-05
MYC#460965.22228187160944.92821127172503e-050.00085469521256674
NR3C1#2908614.9730233311738.86442195171695e-085.24825036403269e-06
POLR2A#543062.147453176558070.01019570676818780.0380744956256576
RAD21#5885610.35503389545638.10515055094479e-073.54626652027701e-05
SMC3#9126615.04493284493288.61317699636729e-085.12857236216421e-06
TAF1#687263.343046285745290.0007162474284635620.00573827594210693
TCF7L2#6934610.77017656313736.40204410218762e-072.91593146091745e-05
TFAP2A#7020616.5186343730454.91595718330683e-083.16143874548881e-06
TFAP2C#7022610.80922860986026.2644941908553e-072.8670355337368e-05
USF1#739166.361499277207961.50818327938273e-050.000357091710531519
USF2#7392612.99219738506962.07721573629339e-071.11423900504748e-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.

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