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Coexpression cluster:C4484: Difference between revisions

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|full_id=C4484_smallcell_gastric_keratoacanthoma_kidney_small_renal_clear
|full_id=C4484_smallcell_gastric_keratoacanthoma_kidney_small_renal_clear
|id=C4484
|id=C4484
|ontology_enrichment_celltype=CL:0000860!4.76e-14!45;CL:0002057!3.53e-13!42;CL:0002194!7.24e-10!63;CL:0000576!7.24e-10!63;CL:0000040!7.24e-10!63;CL:0000559!7.24e-10!63;CL:0000066!3.23e-09!254;CL:0002009!3.47e-09!65;CL:0000839!3.61e-08!70;CL:0000557!2.01e-07!71;CL:0000766!2.74e-07!76
|ontology_enrichment_celltype=CL:0000860!1.57e-08!42;CL:0002057!1.57e-08!42;CL:0000066!1.74e-07!253;CL:0000473!9.57e-07!48;CL:0000234!9.57e-07!48
|ontology_enrichment_disease=DOID:305!1.67e-13!106;DOID:299!1.32e-08!25;DOID:0050687!9.88e-08!143
|ontology_enrichment_disease=DOID:305!1.32e-14!106;DOID:299!9.60e-09!25;DOID:0050687!1.61e-08!143
|ontology_enrichment_uberon=UBERON:0000062!2.72e-13!511;UBERON:0001737!2.47e-09!9;UBERON:0004119!1.77e-08!169;UBERON:0000925!1.77e-08!169;UBERON:0006595!1.77e-08!169;UBERON:0005631!4.45e-08!14;UBERON:0000158!4.45e-08!14;UBERON:0001007!6.57e-08!155;UBERON:0001555!6.57e-08!155;UBERON:0007026!6.57e-08!155;UBERON:0004921!1.67e-07!129;UBERON:0004185!1.67e-07!129
|ontology_enrichment_uberon=UBERON:0001737!4.51e-12!9;UBERON:0000062!8.52e-12!503;UBERON:0001007!1.56e-09!145;UBERON:0001555!1.56e-09!145;UBERON:0007026!1.56e-09!145;UBERON:0004921!2.85e-09!118;UBERON:0001557!6.37e-09!19;UBERON:0008947!6.46e-09!38;UBERON:0003258!6.46e-09!38;UBERON:0004119!1.76e-08!160;UBERON:0000925!1.76e-08!160;UBERON:0006595!1.76e-08!160;UBERON:0005631!4.02e-08!14;UBERON:0000158!4.02e-08!14;UBERON:0000065!2.97e-07!54;UBERON:0001004!3.21e-07!74;UBERON:0001041!4.84e-07!87;UBERON:0000072!8.64e-07!47
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280891124212814!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327122810750503!ELK4#2005;3:16.235681658468:0.000233604395574599:0.0025619457596782!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000678599155776868!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00435434902939678!IRF3#3661;3:46.9819522114896:9.63568551583244e-06:0.000254062448772538!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445826022656911!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157417887241785!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00722353472774555!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.0048608226982139!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.000302472523001546!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155264753829513!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249219193623836!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618134790389564
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280891124212814!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327122810750503!ELK4#2005;3:16.235681658468:0.000233604395574599:0.0025619457596782!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000678599155776868!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00435434902939678!IRF3#3661;3:46.9819522114896:9.63568551583244e-06:0.000254062448772538!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445826022656911!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157417887241785!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00722353472774555!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.0048608226982139!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.000302472523001546!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155264753829513!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249219193623836!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618134790389564
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}}
}}

Revision as of 15:59, 19 October 2012


Full id: C4484_smallcell_gastric_keratoacanthoma_kidney_small_renal_clear



Phase1 CAGE Peaks

Hg19::chr5:16508972..16508984,-p15@FAM134B
Hg19::chr5:16509015..16509033,-p6@FAM134B
Hg19::chr5:16509062..16509075,-p8@FAM134B


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
classical monocyte1.57e-0842
CD14-positive, CD16-negative classical monocyte1.57e-0842
epithelial cell1.74e-07253
defensive cell9.57e-0748
phagocyte9.57e-0748
Uber Anatomy
Ontology termp-valuen
larynx4.51e-129
organ8.52e-12503
digestive system1.56e-09145
digestive tract1.56e-09145
primitive gut1.56e-09145
subdivision of digestive tract2.85e-09118
upper respiratory tract6.37e-0919
respiratory primordium6.46e-0938
endoderm of foregut6.46e-0938
endoderm-derived structure1.76e-08160
endoderm1.76e-08160
presumptive endoderm1.76e-08160
extraembryonic membrane4.02e-0814
membranous layer4.02e-0814
respiratory tract2.97e-0754
respiratory system3.21e-0774
foregut4.84e-0787
segment of respiratory tract8.64e-0747
Disease
Ontology termp-valuen
carcinoma1.32e-14106
adenocarcinoma9.60e-0925
cell type cancer1.61e-08143


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#1066435.360256373075030.0064925092527670.0280891124212814
E2F1#186934.907389214879320.008460985347239390.0327122810750503
ELK4#2005316.2356816584680.0002336043955745990.0025619457596782
ESR1#2099330.76860329615453.43136389821584e-050.000678599155776868
GTF2F1#2962312.73966087675770.0004835525047438590.00435434902939678
IRF3#3661346.98195221148969.63568551583244e-060.000254062448772538
JUN#3725312.51282919233630.0005103313992726250.00445826022656911
JUND#372736.994663941871030.002921845042734990.0157417887241785
MXI1#460139.96157162875930.001011470541259020.00722353472774555
RFX5#5993312.04791082719510.0005717246050312580.0048608226982139
SMARCC1#6599343.66335931963151.20046018043203e-050.000302472523001546
STAT1#6772320.70658749719920.0001125992441046670.00155264753829513
TFAP2A#7020316.5186343730450.0002218033880766340.00249219193623836
TFAP2C#7022310.80922860986020.0007916746575753130.00618134790389564



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.