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Coexpression cluster:C4725: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191225825873509!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115826145647594!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.0066296866662201!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327851017949889!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00439037221088007!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324446372116771!EP300#2033;3:6.7739417262232:0.00321688050010379:0.016853161903704!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00902092205865151!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00584307517236681!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00389544448038599!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00439059056326336!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.00085500856104621!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00436074087237233!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00393643710030664!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109261148001081!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00446498291100224!JUNB#3726;3:30.6106326598211:3.4847716247536e-05:0.000682953769408222!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157718924135931!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187458024178653!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00723590464131454!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296166855564159!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00668893322938192!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00486914670348688!SMARCA4#6597;3:156.765903307888:2.58908533335753e-07:1.34194284432023e-05!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00204131943022792!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.000302691600154855!SMARCC2#6601;3:94.1553744268976:1.19621075407887e-06:4.86870829872342e-05!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310936691084289!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155387849564578!STAT2#6773;3:65.2637711864407:3.59360517547754e-06:0.000118619636827338!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064568188524584!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.000722927418656304!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249514477028604!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.0061901407174147!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331360277547588
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}}
}}

Revision as of 16:55, 26 November 2012


Full id: C4725_Corneal_Keratinocyte_mesothelioma_Bronchial_Urothelial_papillotubular_Gingival



Phase1 CAGE Peaks

Hg19::chr8:124194824..124194835,+p5@FAM83A
Hg19::chr8:124194875..124194920,+p2@FAM83A
Hg19::chr8:124194922..124194957,+p1@FAM83A


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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.73e-24160
endoderm4.73e-24160
presumptive endoderm4.73e-24160
respiratory system5.57e-2074
respiratory tract6.24e-1954
digestive system5.99e-18145
digestive tract5.99e-18145
primitive gut5.99e-18145
segment of respiratory tract6.20e-1647
respiratory primordium9.28e-1538
endoderm of foregut9.28e-1538
subdivision of digestive tract2.48e-14118
foregut3.63e-1287
endo-epithelium2.64e-1182
epithelial bud7.50e-1137
orifice1.09e-1036
reproductive structure8.48e-1059
reproductive system8.48e-1059
upper respiratory tract1.90e-0919
epithelial fold3.50e-0947
anatomical space8.34e-0995
renal system8.88e-0948
thoracic cavity element8.95e-0934
thoracic cavity8.95e-0934
larynx9.99e-099
thoracic segment organ2.35e-0835
extraembryonic membrane2.42e-0814
membranous layer2.42e-0814
urinary system structure3.32e-0847
primordium5.09e-08160
respiratory system epithelium1.08e-0728
female organism1.64e-0741
organ part1.83e-07218
reproductive organ2.13e-0748
tracheobronchial tree3.42e-0715
lower respiratory tract3.42e-0715
urothelium3.69e-075
internal genitalia6.17e-0725
immaterial anatomical entity7.73e-07117
Disease
Ontology termp-valuen
carcinoma2.32e-20106
cell type cancer9.08e-14143
squamous cell carcinoma2.30e-1014
cancer8.35e-10235
disease of cellular proliferation3.55e-09239


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
CCNT2#90536.336201576962630.003930750035764890.0191225825873509
CEBPB#105137.971147625824820.001974187055288560.0115826145647594
CHD2#1106310.34402283411690.0009033701102746880.0066296866662201
E2F1#186934.907389214879320.008460985347239390.0327851017949889
E2F4#1874312.66806031528440.0004917987006298980.00439037221088007
E2F6#187635.017155731697390.00791769806886330.0324446372116771
EP300#203336.77394172622320.003216880500103790.016853161903704
FOS#235338.99795530889440.001372499272417130.00902092205865151
FOXA1#3169311.08141974938550.000734755275698670.00584307517236681
GATA1#2623313.56030814380040.0004009615963782630.00389544448038599
GATA2#2624312.7449317335540.0004829527704283790.00439059056326336
GATA3#2625327.2365163572064.94721007899563e-050.00085500856104621
GTF2F1#2962312.73966087675770.0004835525047438590.00436074087237233
HDAC2#3066313.41562023662630.0004140761399857210.00393643710030664
HMGN3#932438.178547723350590.001827766942164210.0109261148001081
JUN#3725312.51282919233630.0005103313992726250.00446498291100224
JUNB#3726330.61063265982113.4847716247536e-050.000682953769408222
JUND#372736.994663941871030.002921845042734990.0157718924135931
MAX#414936.452555509007120.003721913834265510.0187458024178653
MXI1#460139.96157162875930.001011470541259020.00723590464131454
MYC#460935.22228187160940.007020843755740150.0296166855564159
RAD21#5885310.35503389545630.0009004912073565420.00668893322938192
RFX5#5993312.04791082719510.0005717246050312580.00486914670348688
SMARCA4#65973156.7659033078882.58908533335753e-071.34194284432023e-05
SMARCB1#6598318.25271578115740.000164397760679890.00204131943022792
SMARCC1#6599343.66335931963151.20046018043203e-050.000302691600154855
SMARCC2#6601394.15537442689761.19621075407887e-064.86870829872342e-05
SMC3#9126315.04493284493280.0002935825420371870.00310936691084289
STAT1#6772320.70658749719920.0001125992441046670.00155387849564578
STAT2#6773365.26377118644073.59360517547754e-060.000118619636827338
STAT3#6774310.51946499715420.0008589184530415310.0064568188524584
TAL1#6886329.86861667744023.75103522793067e-050.000722927418656304
TFAP2A#7020316.5186343730450.0002218033880766340.00249514477028604
TFAP2C#7022310.80922860986020.0007916746575753130.0061901407174147
YY1#752834.911170749853860.008441455341808260.0331360277547588



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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