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Coexpression cluster:C3036: Difference between revisions

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|ontology_enrichment_disease=DOID:162!5.42e-26!235;DOID:14566!2.65e-24!239;DOID:2531!1.22e-13!51;DOID:0060083!1.22e-13!51;DOID:0050687!3.46e-13!143;DOID:0050686!1.09e-12!137;DOID:1240!3.62e-12!39;DOID:305!1.51e-10!106;DOID:8692!7.53e-10!31
|ontology_enrichment_disease=DOID:162!5.42e-26!235;DOID:14566!2.65e-24!239;DOID:2531!1.22e-13!51;DOID:0060083!1.22e-13!51;DOID:0050687!3.46e-13!143;DOID:0050686!1.09e-12!137;DOID:1240!3.62e-12!39;DOID:305!1.51e-10!106;DOID:8692!7.53e-10!31
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tf_chipseq_enrich=BCL3#602;3:34.5471028037383:2.42397750207122e-05:0.000526206165742707!BCLAF1#9774;3:21.6526476101218:9.8473954032885e-05:0.00138811192944263!BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296072306613639!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189076825251128!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323435031177605!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00435205596467429!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320286803243479!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0318946046237894!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0459873838889061!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0166799614015659!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00759622569692998!FOSL2#2355;2:11.2868004030411:0.010053458697312:0.0376563918118052!GTF2B#2959;3:31.9438299343242:3.06634405746243e-05:0.00062572471085838!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00432674263561891!HNF4G#3174;2:19.1689483509645:0.00354398661128422:0.0179657517569125!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127582838549647!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156121239342167!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185640650908284!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.0324685055553606!MEF2C#4208;2:27.5409029950827:0.00172911993836969:0.0106447130706391!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293100651958966!NANOG#79923;2:19.4965189873418:0.00342725564850102:0.0174417285193353!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268470397928542!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00307821802712234!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00469238378100564!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172214796083612!PBX3#5090;2:14.6096751244961:0.00605612247321789:0.0268051947355655!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.008792884572643!RDBP#7936;3:153.638403990025:2.75057764221434e-07:1.39653659881003e-05!REST#5978;3:9.65002871612802:0.00111263624711459:0.00765195686898463!RXRA#6256;2:13.3830780927555:0.00719643442946573:0.029815471889042!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275321681276369!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245363212157255!STAT2#6773;2:43.5091807909604:0.000696899089886823:0.00560605746350535!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00540383539066079!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00627579423211213!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0328898315031959!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189447652434937!WRNIP1#56897;2:73.2133095662507:0.00024709364113596:0.00268451188875465!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0327799648426515!ZBTB33#10009;3:31.6647250299812:3.14815888737575e-05:0.000632898105945402!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00241840653976096
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}}
}}

Revision as of 14:25, 5 September 2012


Full id: C3036_Mast_CD14_diffuse_Reticulocytes_chronic_acute_teratocarcinoma



Phase1 CAGE Peaks

Hg19::chr10:70091812..70091830,+p1@HNRNPH3
Hg19::chr10:70091847..70091858,+p2@HNRNPH3
Hg19::chr7:26240357..26240377,-p1@HNRNPA2B1


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


GO IDGO nameFDR corrected p-value
GO:0043047single-stranded telomeric DNA binding0.00565171317555634
GO:0042162telomeric DNA binding0.00847756976333451
GO:0030530heterogeneous nuclear ribonucleoprotein complex0.00847756976333451
GO:0003697single-stranded DNA binding0.0118172184579814
GO:0000375RNA splicing, via transesterification reactions0.0118172184579814
GO:0000398nuclear mRNA splicing, via spliceosome0.0118172184579814
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0118172184579814
GO:0050658RNA transport0.0118172184579814
GO:0051236establishment of RNA localization0.0118172184579814
GO:0050657nucleic acid transport0.0118172184579814
GO:0006403RNA localization0.0118172184579814
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0122453785470387
GO:0005681spliceosome0.0151074640654294
GO:0043566structure-specific DNA binding0.0160468284805975
GO:0008380RNA splicing0.0211939244083363
GO:0006397mRNA processing0.0241080890144825
GO:0016071mRNA metabolic process0.0284247927358863
GO:0006396RNA processing0.041210408571765



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>


Disease
Ontology termp-valuen
cancer5.42e-26235
disease of cellular proliferation2.65e-24239
hematologic cancer1.22e-1351
immune system cancer1.22e-1351
cell type cancer3.46e-13143
organ system cancer1.09e-12137
leukemia3.62e-1239
carcinoma1.51e-10106
myeloid leukemia7.53e-1031


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#602334.54710280373832.42397750207122e-050.000526206165742707
BCLAF1#9774321.65264761012189.8473954032885e-050.00138811192944263
BRCA1#672213.45615376214920.007119807716084560.0296072306613639
CCNT2#90536.336201576962630.003930750035764890.0189076825251128
E2F1#186934.907389214879320.008460985347239390.0323435031177605
E2F4#1874312.66806031528440.0004917987006298980.00435205596467429
E2F6#187635.017155731697390.00791769806886330.0320286803243479
EGR1#195834.988179094810140.008056488137383440.0318946046237894
ELF1#199734.258097958807540.01295179875054610.0459873838889061
EP300#203336.77394172622320.003216880500103790.0166799614015659
ETS1#211339.728760922202340.001085840092584840.00759622569692998
FOSL2#2355211.28680040304110.0100534586973120.0376563918118052
GTF2B#2959331.94382993432423.06634405746243e-050.00062572471085838
GTF2F1#2962312.73966087675770.0004835525047438590.00432674263561891
HNF4G#3174219.16894835096450.003543986611284220.0179657517569125
IRF1#365937.63716375356390.002244692747297240.0127582838549647
JUND#372736.994663941871030.002921845042734990.0156121239342167
MAX#414936.452555509007120.003721913834265510.0185640650908284
MEF2A#4205212.4954872730960.008235029478029740.0324685055553606
MEF2C#4208227.54090299508270.001729119938369690.0106447130706391
MYC#460935.22228187160940.007020843755740150.0293100651958966
NANOG#79923219.49651898734180.003427255648501020.0174417285193353
NFKB1#479035.488063424193840.006049381815655430.0268470397928542
NR3C1#2908314.9730233311730.0002978331194675480.00307821802712234
NRF1#4899312.21027944771090.0005492172401020010.00469238378100564
PAX5#507936.669565531177830.003370290999677260.0172214796083612
PBX3#5090214.60967512449610.006056122473217890.0268051947355655
POU2F2#545239.106124057742520.001324165192682130.008792884572643
RDBP#79363153.6384039900252.75057764221434e-071.39653659881003e-05
REST#597839.650028716128020.001112636247114590.00765195686898463
RXRA#6256213.38307809275550.007196434429465730.029815471889042
SIN3A#2594235.408884726815140.006318961977991520.0275321681276369
SP1#666735.69838137814090.005403962701712170.0245363212157255
STAT2#6773243.50918079096040.0006968990898868230.00560605746350535
TAF7#6879311.43306940492390.0006690181981945830.00540383539066079
TCF12#6938310.63446490218640.0008313523990202070.00627579423211213
TRIM28#10155212.39368336350830.008368344129438470.0328898315031959
USF1#739136.361499277207960.00388404057290560.0189447652434937
WRNIP1#56897273.21330956625070.000247093641135960.00268451188875465
YY1#752834.911170749853860.008441455341808260.0327799648426515
ZBTB33#10009331.66472502998123.14815888737575e-050.000632898105945402
ZEB1#6935316.88843201754390.0002075486917327580.00241840653976096



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.