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Coexpression cluster:C3982: Difference between revisions

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|tf_chipseq_enrich=BCLAF1#9774;3:21.6526476101218:9.8473954032885e-05:0.0013926230582587!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190233365609476!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171951146192947!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325712071021133!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00437615783378086!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322610981825068!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320965693145218!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462816200673447!ELK4#2005;3:16.235681658468:0.000233604395574599:0.00255845317422562!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.0076304705577626!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154259961029346!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00434423570261883!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108818921259086!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.012821782204932!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156932154496374!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186755529420993!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294844947929449!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.026981183269783!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00471514174591146!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173061518125421!REST#5978;3:9.65002871612802:0.00111263624711459:0.00768383369783777!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00485055613524448!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277113613277118!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246800971053051!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.01091403336655!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00375338997998061!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064313582102957!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00543705482851483!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248390778976363!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00616245878829158!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000647471327277562!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190506416847644!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329761419279264!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140367079260773!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00389422987821642
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}}
}}

Revision as of 16:28, 26 November 2012


Full id: C3982_adult_biphenotypic_NK_signet_acute_cord_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr1:45205560..45205575,+p2@KIF2C
Hg19::chr1:45205577..45205589,+p3@KIF2C
Hg19::chr1:45205591..45205598,+p5@KIF2C


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><br>disease_data<br>

Cell Type
Ontology termp-valuen
animal cell1.26e-16679
eukaryotic cell1.26e-16679
epithelial cell1.29e-11253
native cell1.47e-11722
Disease
Ontology termp-valuen
cancer6.75e-49235
disease of cellular proliferation2.71e-48239
organ system cancer4.74e-26137
hematologic cancer1.60e-2351
immune system cancer1.60e-2351
cell type cancer2.07e-22143
leukemia3.80e-1739
carcinoma4.42e-17106
myeloid leukemia4.68e-1331
lymphoma1.85e-0710


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
BCLAF1#9774321.65264761012189.8473954032885e-050.0013926230582587
CCNT2#90536.336201576962630.003930750035764890.0190233365609476
CTCFL#140690319.74647435897440.0001298372005551160.00171951146192947
E2F1#186934.907389214879320.008460985347239390.0325712071021133
E2F4#1874312.66806031528440.0004917987006298980.00437615783378086
E2F6#187635.017155731697390.00791769806886330.0322610981825068
EGR1#195834.988179094810140.008056488137383440.0320965693145218
ELF1#199734.258097958807540.01295179875054610.0462816200673447
ELK4#2005316.2356816584680.0002336043955745990.00255845317422562
ETS1#211339.728760922202340.001085840092584840.0076304705577626
GABPB1#255337.067683836182170.002832212825417420.0154259961029346
GTF2F1#2962312.73966087675770.0004835525047438590.00434423570261883
HMGN3#932438.178547723350590.001827766942164210.0108818921259086
IRF1#365937.63716375356390.002244692747297240.012821782204932
JUND#372736.994663941871030.002921845042734990.0156932154496374
MAX#414936.452555509007120.003721913834265510.0186755529420993
MYC#460935.22228187160940.007020843755740150.0294844947929449
NFKB1#479035.488063424193840.006049381815655430.026981183269783
NRF1#4899312.21027944771090.0005492172401020010.00471514174591146
PAX5#507936.669565531177830.003370290999677260.0173061518125421
REST#597839.650028716128020.001112636247114590.00768383369783777
RFX5#5993312.04791082719510.0005717246050312580.00485055613524448
SIN3A#2594235.408884726815140.006318961977991520.0277113613277118
SP1#666735.69838137814090.005403962701712170.0246800971053051
SPI1#668838.204323508522730.001810593189410520.01091403336655
SRF#6722313.79717826216780.0003806615025800190.00375338997998061
STAT3#6774310.51946499715420.0008589184530415310.0064313582102957
TAF7#6879311.43306940492390.0006690181981945830.00543705482851483
TFAP2A#7020316.5186343730450.0002218033880766340.00248390778976363
TFAP2C#7022310.80922860986020.0007916746575753130.00616245878829158
THAP1#55145331.36914460285133.23800758564397e-050.000647471327277562
USF1#739136.361499277207960.00388404057290560.0190506416847644
YY1#752834.911170749853860.008441455341808260.0329761419279264
ZBTB7A#5134137.35190930787590.002516255860282270.0140367079260773
ZNF143#7702313.50087655222790.0004062804962997170.00389422987821642



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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