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Coexpression cluster:C3686: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!1.36e-20!375;UBERON:0002204!1.97e-18!167;UBERON:0002371!3.53e-17!80;UBERON:0001474!7.25e-17!86;UBERON:0004765!7.84e-16!101;UBERON:0001434!7.84e-16!101;UBERON:0000926!8.01e-13!448;UBERON:0004120!8.01e-13!448;UBERON:0006603!8.01e-13!448;UBERON:0003081!1.46e-11!216;UBERON:0002390!6.27e-10!102;UBERON:0003061!6.27e-10!102;UBERON:0002405!2.61e-09!115;UBERON:0002193!3.76e-09!112;UBERON:0000479!2.41e-08!787;UBERON:0002199!7.18e-08!45;UBERON:0002416!7.18e-08!45;UBERON:0002097!9.39e-08!40;UBERON:0000062!1.13e-07!511;UBERON:0003102!2.13e-07!95
|ontology_enrichment_uberon=UBERON:0002384!1.36e-20!375;UBERON:0002204!1.97e-18!167;UBERON:0002371!3.53e-17!80;UBERON:0001474!7.25e-17!86;UBERON:0004765!7.84e-16!101;UBERON:0001434!7.84e-16!101;UBERON:0000926!8.01e-13!448;UBERON:0004120!8.01e-13!448;UBERON:0006603!8.01e-13!448;UBERON:0003081!1.46e-11!216;UBERON:0002390!6.27e-10!102;UBERON:0003061!6.27e-10!102;UBERON:0002405!2.61e-09!115;UBERON:0002193!3.76e-09!112;UBERON:0000479!2.41e-08!787;UBERON:0002199!7.18e-08!45;UBERON:0002416!7.18e-08!45;UBERON:0002097!9.39e-08!40;UBERON:0000062!1.13e-07!511;UBERON:0003102!2.13e-07!95
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321845042857593!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00914524824392107!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461820727111056!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167364642099402!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00897011586432869!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000370882404499511!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0153978904359068!GTF2B#2959;3:31.9438299343242:3.06634405746243e-05:0.000627686999249939!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00433528543591243!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00391009927522321!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443895236184173!JUNB#3726;3:30.6106326598211:3.4847716247536e-05:0.000680018803657776!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156609994569258!MAX#4149;3:6.45255550900712:0.00372191383426551:0.018636156819295!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00719843079104266!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294265150094609!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269409145642078!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308738393688052!REST#5978;3:9.65002871612802:0.00111263624711459:0.0076691273107445!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00484268824208107!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276405624903441!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109014494470682!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00154815066548806!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00642490934803069!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613238629217483!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615374438542037!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329023009682072!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140052891596685
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}}
}}

Revision as of 12:31, 5 September 2012


Full id: C3686_CD14_Mesenchymal_liposarcoma_renal_amniotic_anaplastic_immature



Phase1 CAGE Peaks

Hg19::chr17:75315624..75315648,+p11@SEPT9
Hg19::chr17:75315654..75315688,+p6@SEPT9
Hg19::chr17:75315696..75315710,+p19@SEPT9


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>


Uber Anatomy
Ontology termp-valuen
connective tissue1.36e-20375
musculoskeletal system1.97e-18167
bone marrow3.53e-1780
bone element7.25e-1786
skeletal element7.84e-16101
skeletal system7.84e-16101
mesoderm8.01e-13448
mesoderm-derived structure8.01e-13448
presumptive mesoderm8.01e-13448
lateral plate mesoderm1.46e-11216
hematopoietic system6.27e-10102
blood island6.27e-10102
immune system2.61e-09115
hemolymphoid system3.76e-09112
tissue2.41e-08787
integument7.18e-0845
integumental system7.18e-0845
skin of body9.39e-0840
organ1.13e-07511
surface structure2.13e-0795


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#187635.017155731697390.00791769806886330.0321845042857593
EBF1#187938.9064668465690.00141523283560980.00914524824392107
ELF1#199734.258097958807540.01295179875054610.0461820727111056
EP300#203336.77394172622320.003216880500103790.0167364642099402
FOS#235338.99795530889440.001372499272417130.00897011586432869
FOSL1#8061339.7135797163731.59554825631833e-050.000370882404499511
GABPB1#255337.067683836182170.002832212825417420.0153978904359068
GTF2B#2959331.94382993432423.06634405746243e-050.000627686999249939
GTF2F1#2962312.73966087675770.0004835525047438590.00433528543591243
HDAC2#3066313.41562023662630.0004140761399857210.00391009927522321
JUN#3725312.51282919233630.0005103313992726250.00443895236184173
JUNB#3726330.61063265982113.4847716247536e-050.000680018803657776
JUND#372736.994663941871030.002921845042734990.0156609994569258
MAX#414936.452555509007120.003721913834265510.018636156819295
MXI1#460139.96157162875930.001011470541259020.00719843079104266
MYC#460935.22228187160940.007020843755740150.0294265150094609
NFKB1#479035.488063424193840.006049381815655430.0269409145642078
NR3C1#2908314.9730233311730.0002978331194675480.00308738393688052
REST#597839.650028716128020.001112636247114590.0076691273107445
RFX5#5993312.04791082719510.0005717246050312580.00484268824208107
SIN3A#2594235.408884726815140.006318961977991520.0276405624903441
SPI1#668838.204323508522730.001810593189410520.0109014494470682
STAT1#6772320.70658749719920.0001125992441046670.00154815066548806
STAT3#6774310.51946499715420.0008589184530415310.00642490934803069
TCF7L2#6934310.77017656313730.0008003181298398380.00613238629217483
TFAP2C#7022310.80922860986020.0007916746575753130.00615374438542037
YY1#752834.911170749853860.008441455341808260.0329023009682072
ZBTB7A#5134137.35190930787590.002516255860282270.0140052891596685



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.