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Coexpression cluster:C2909: Difference between revisions

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|tf_chipseq_enrich=BCL3#602;4:34.5471028037383:7.01262157705428e-07:3.15549842691069e-05!BCLAF1#9774;4:21.6526476101218:4.54636978835329e-06:0.000141948673938963!CCNT2#905;4:6.33620157696263:0.000620310058721564:0.0051375544982412!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268735718331689!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00820144022002712!CTCFL#140690;4:19.7464743589744:6.5732084880439e-06:0.000193598229352176!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106813294762121!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.000728307022658933!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00999557452943528!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101682050914181!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161294754018801!ELK4#2005;4:16.235681658468:1.43847748454449e-05:0.000343704301094354!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00435518042760734!ETS1#2113;4:9.72876092220234:0.000111595531741814:0.0015486215439255!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195537566666757!FOSL1#8061;4:39.713579716373:4.01511434669553e-07:1.94046518859109e-05!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00390951245182634!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.000719437278750136!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186658607434054!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248616475909959!HNF4A#3172;4:23.1322903629537:3.48990320893214e-06:0.000115855690158189!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.0030807083459562!IRF4#3662;4:21.9145126867441:4.33289161192893e-06:0.000136837879364453!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000745311937753712!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392677306911105!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486719258678102!MEF2A#4205;4:18.7432309096441:8.0978922767748e-06:0.000224750404330078!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142800078359959!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00890061677018444!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00769469388402489!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.000795663521441344!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.0044498413145009!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188820913643428!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157591563250571!SETDB1#9869;4:40.3200261780105:3.77887289069054e-07:1.8537421598442e-05!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00798290621638558!SIX5#147912;4:17.086715355459:1.17257016123224e-05:0.000297888725538637!SMARCC1#6599;4:43.6633593196315:2.74744977017458e-07:1.40795341779815e-05!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00685793154807434!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000585896573070899!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123549743141698!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323381797081996!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.000972052826174345!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245092118657567!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.0011579612874939!THAP1#55145;4:31.3691446028513:1.03171810326891e-06:4.32737377459043e-05!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000231122047416127!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00509225529522298!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107100971925251!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00347341927072206!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00250053707888056
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}}
}}

Revision as of 15:48, 26 November 2012


Full id: C2909_lymphoma_adenocarcinoma_chronic_acute_diffuse_nonsmall_CD19



Phase1 CAGE Peaks

Hg19::chr7:96746988..96747028,+p1@ACN9
Hg19::chr7:96747030..96747041,+p4@ACN9
Hg19::chr7:96747044..96747055,+p3@ACN9
Hg19::chr7:96747057..96747073,+p2@ACN9


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
nucleate cell4.99e-0855
lymphocyte1.34e-0753
common lymphoid progenitor1.34e-0753
lymphoid lineage restricted progenitor cell3.74e-0752
Disease
Ontology termp-valuen
hematologic cancer1.45e-2251
immune system cancer1.45e-2251
cancer3.87e-22235
disease of cellular proliferation2.61e-20239
leukemia9.46e-1839
organ system cancer9.24e-15137
myeloid leukemia1.61e-1431
carcinoma1.65e-10106
cell type cancer2.01e-10143


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
BCL3#602434.54710280373837.01262157705428e-073.15549842691069e-05
BCLAF1#9774421.65264761012184.54636978835329e-060.000141948673938963
CCNT2#90546.336201576962630.0006203100587215640.0051375544982412
CEBPB#105147.971147625824820.0002476385788090830.00268735718331689
CTCF#1066445.360256373075030.001211145381643620.00820144022002712
CTCFL#140690419.74647435897446.5732084880439e-060.000193598229352176
E2F1#186944.907389214879320.001724022357361790.0106813294762121
E2F4#1874412.66806031528443.88145892637771e-050.000728307022658933
E2F6#187645.017155731697390.00157802193473060.00999557452943528
EGR1#195844.988179094810140.001615011500076050.0101682050914181
ELF1#199744.258097958807540.003041525565781240.0161294754018801
ELK4#2005416.2356816584681.43847748454449e-050.000343704301094354
EP300#203346.77394172622320.0004748459821442640.00435518042760734
ETS1#211349.728760922202340.0001115955317418140.0015486215439255
FOS#235348.99795530889440.0001525147711168630.00195537566666757
FOSL1#8061439.7135797163734.01511434669553e-071.94046518859109e-05
GABPB1#255347.067683836182170.0004006876864423170.00390951245182634
GTF2F1#2962412.73966087675773.79492332235515e-050.000719437278750136
HEY1#2346244.040111043105710.00375304636917980.0186658607434054
HMGN3#932448.178547723350590.0002234570284440470.00248616475909959
HNF4A#3172423.13229036295373.48990320893214e-060.000115855690158189
IRF1#365947.63716375356390.0002938853996185490.0030807083459562
IRF4#3662421.91451268674414.33289161192893e-060.000136837879364453
JUN#3725412.51282919233634.07770316866756e-050.000745311937753712
JUND#372746.994663941871030.000417684217818580.00392677306911105
MAX#414946.452555509007120.0005767613195645490.00486719258678102
MEF2A#4205418.74323090964418.0978922767748e-060.000224750404330078
MXI1#460149.96157162875930.0001015224754950450.00142800078359959
MYC#460945.22228187160940.001344309395272740.00890061677018444
NFKB1#479045.488063424193840.001102199566301980.00769469388402489
NRF1#4899412.21027944771094.49717228915276e-050.000795663521441344
PAX5#507946.669565531177830.0005052774169483260.0044498413145009
POU2F2#545249.106124057742520.000145395665174930.00188820913643428
REST#597849.650028716128020.0001152825614219170.00157591563250571
SETDB1#9869440.32002617801053.77887289069054e-071.8537421598442e-05
SIN3A#2594245.408884726815140.001168172384885160.00798290621638558
SIX5#147912417.0867153554591.17257016123224e-050.000297888725538637
SMARCC1#6599443.66335931963152.74744977017458e-071.40795341779815e-05
SP1#666745.69838137814090.0009482606065333980.00685793154807434
SRF#6722413.79717826216782.75840773062708e-050.000585896573070899
STAT3#6774410.51946499715428.16377768286615e-050.00123549743141698
TAF1#687243.343046285745290.008005664898701650.0323381797081996
TAF7#6879411.43306940492395.85061525419808e-050.000972052826174345
TBP#690843.706770687096390.005296377814784350.0245092118657567
TCF7L2#6934410.77017656313737.42969445082454e-050.0011579612874939
THAP1#55145431.36914460285131.03171810326891e-064.32737377459043e-05
TRIM28#10155418.59052504526258.36730015875654e-060.000231122047416127
USF1#739146.361499277207960.0006105011399140830.00509225529522298
YY1#752844.911170749853860.00171871838055440.0107100971925251
ZBTB7A#5134147.35190930787590.000342223540015990.00347341927072206
ZNF263#1012748.221841637010680.0002187871180958320.00250053707888056



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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