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Coexpression cluster:C2552: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!5.52e-23!115;UBERON:0001049!3.28e-14!57;UBERON:0005068!3.28e-14!57;UBERON:0006241!3.28e-14!57;UBERON:0007135!3.28e-14!57;UBERON:0001017!5.11e-14!82;UBERON:0005743!5.04e-13!86;UBERON:0000955!2.43e-12!69;UBERON:0006238!2.43e-12!69;UBERON:0002616!5.76e-12!59;UBERON:0000073!2.05e-11!94;UBERON:0001016!2.05e-11!94;UBERON:0003080!2.42e-11!42;UBERON:0002780!3.38e-11!41;UBERON:0001890!3.38e-11!41;UBERON:0006240!3.38e-11!41;UBERON:0001893!2.36e-10!34;UBERON:0002020!3.69e-10!34;UBERON:0003528!3.69e-10!34;UBERON:0002791!7.87e-10!33;UBERON:0001869!2.49e-09!32;UBERON:0003075!2.16e-07!86;UBERON:0007284!2.16e-07!86;UBERON:0002619!3.81e-07!22;UBERON:0002346!9.53e-07!90
|ontology_enrichment_uberon=UBERON:0007023!2.45e-24!114;UBERON:0001049!4.65e-16!56;UBERON:0005068!4.65e-16!56;UBERON:0006241!4.65e-16!56;UBERON:0007135!4.65e-16!56;UBERON:0001017!5.99e-16!81;UBERON:0001016!1.89e-14!89;UBERON:0000073!2.08e-14!53;UBERON:0002616!2.08e-14!53;UBERON:0000955!5.36e-14!68;UBERON:0006238!5.36e-14!68;UBERON:0002780!2.76e-13!41;UBERON:0001890!2.76e-13!41;UBERON:0003080!2.76e-13!41;UBERON:0006240!2.76e-13!41;UBERON:0001893!1.63e-12!34;UBERON:0003528!3.05e-12!34;UBERON:0002020!3.05e-12!34;UBERON:0001869!3.32e-11!32;UBERON:0002791!3.84e-11!32;UBERON:0003075!7.45e-11!82;UBERON:0007284!7.45e-11!82;UBERON:0002346!4.61e-10!86;UBERON:0010371!3.26e-08!104;UBERON:0001950!3.43e-08!20;UBERON:0002619!4.73e-08!22;UBERON:0003056!1.31e-07!61;UBERON:0000125!2.52e-07!9;UBERON:0002308!2.52e-07!9;UBERON:0000956!3.68e-07!25;UBERON:0000203!3.68e-07!25
|tf_chipseq_enrich=ATF3#467;4:22.4631745260087:3.92475754624726e-06:0.000127416149633981!BATF#10538;4:24.3578017923036:2.83869198020713e-06:9.78449345613375e-05!BCLAF1#9774;4:21.6526476101218:4.54636978835329e-06:0.000141736810246516!BRCA1#672;4:20.1842306432238:6.02116732184487e-06:0.000179516041657481!CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512414476175128!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.0026823403372995!CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.0012911713206948!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106528914318133!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.0007271312803802!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160967816238283!ESR1#2099;4:30.7686032961545:1.11467714392546e-06:4.60870016763384e-05!ETS1#2113;4:9.72876092220234:0.000111595531741814:0.00154615624032678!FOS#2353;4:8.9979553088944:0.000152514771116863:0.0019496316010617!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00390404154159428!GATA1#2623;4:13.5603081438004:2.95627390049268e-05:0.00061393972935684!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000722180488741566!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186179836484477!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248167041617055!HNF4G#3174;4:28.7534225264468:1.46167379934821e-06:5.67071879383833e-05!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00307700223065279!IRF4#3662;4:21.9145126867441:4.33289161192893e-06:0.000136507652204599!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.00074349029544775!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391865990161289!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00485620569606594!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142473875547258!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00888091143860392!NANOG#79923;4:29.2447784810127:1.36586687657858e-06:5.33669175918409e-05!NFYA#4800;4:18.4255806998305:8.67100748407158e-06:0.000234609158194029!NR2C2#7182;4:32.6146109052409:8.82887529809196e-07:3.82288104169746e-05!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.000794183592673022!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444085400561021!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157118562342994!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000827243062812647!RXRA#6256;4:20.0746171391333:6.1537798808435e-06:0.000182376452036156!SIX5#147912;4:17.086715355459:1.17257016123224e-05:0.000297599161771406!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000241622093300054!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00684607973771198!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249547441741953!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000584707418264585!STAT1#6772;4:20.7065874971992:5.43610708103893e-06:0.000165377683494502!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123174917281257!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322434011937643!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.000969892708782846!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244399064462627!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115503104904683!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.0011457617553119!THAP1#55145;4:31.3691446028513:1.03171810326891e-06:4.31870168285779e-05!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000230269423262286!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508170308053614!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000681432970180591!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106903239203574!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00346802680921113!ZNF143#7702;4:13.5008765522279:3.00867915035614e-05:0.000621240493839551!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249018175967857
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}}
}}

Revision as of 14:09, 19 October 2012


Full id: C2552_seminal_heart_ductus_mature_skeletal_corpus_medulla



Phase1 CAGE Peaks

Hg19::chr1:202317855..202317864,+p10@PPP1R12B
Hg19::chr1:202317869..202317884,+p2@PPP1R12B
Hg19::chr1:202317894..202317903,+p4@PPP1R12B
Hg19::chr1:202317923..202317936,+p5@PPP1R12B


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.45e-24114
neural tube4.65e-1656
neural rod4.65e-1656
future spinal cord4.65e-1656
neural keel4.65e-1656
central nervous system5.99e-1681
nervous system1.89e-1489
regional part of nervous system2.08e-1453
regional part of brain2.08e-1453
brain5.36e-1468
future brain5.36e-1468
regional part of forebrain2.76e-1341
forebrain2.76e-1341
anterior neural tube2.76e-1341
future forebrain2.76e-1341
telencephalon1.63e-1234
brain grey matter3.05e-1234
gray matter3.05e-1234
cerebral hemisphere3.32e-1132
regional part of telencephalon3.84e-1132
neural plate7.45e-1182
presumptive neural plate7.45e-1182
neurectoderm4.61e-1086
ecto-epithelium3.26e-08104
neocortex3.43e-0820
regional part of cerebral cortex4.73e-0822
pre-chordal neural plate1.31e-0761
neural nucleus2.52e-079
nucleus of brain2.52e-079
cerebral cortex3.68e-0725
pallium3.68e-0725


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
ATF3#467422.46317452600873.92475754624726e-060.000127416149633981
BATF#10538424.35780179230362.83869198020713e-069.78449345613375e-05
BCLAF1#9774421.65264761012184.54636978835329e-060.000141736810246516
BRCA1#672420.18423064322386.02116732184487e-060.000179516041657481
CCNT2#90546.336201576962630.0006203100587215640.00512414476175128
CEBPB#105147.971147625824820.0002476385788090830.0026823403372995
CHD2#1106410.34402283411698.73193255208051e-050.0012911713206948
E2F1#186944.907389214879320.001724022357361790.0106528914318133
E2F4#1874412.66806031528443.88145892637771e-050.0007271312803802
ELF1#199744.258097958807540.003041525565781240.0160967816238283
ESR1#2099430.76860329615451.11467714392546e-064.60870016763384e-05
ETS1#211349.728760922202340.0001115955317418140.00154615624032678
FOS#235348.99795530889440.0001525147711168630.0019496316010617
GABPB1#255347.067683836182170.0004006876864423170.00390404154159428
GATA1#2623413.56030814380042.95627390049268e-050.00061393972935684
GATA2#2624412.7449317335543.78864877853583e-050.000722180488741566
HEY1#2346244.040111043105710.00375304636917980.0186179836484477
HMGN3#932448.178547723350590.0002234570284440470.00248167041617055
HNF4G#3174428.75342252644681.46167379934821e-065.67071879383833e-05
IRF1#365947.63716375356390.0002938853996185490.00307700223065279
IRF4#3662421.91451268674414.33289161192893e-060.000136507652204599
JUN#3725412.51282919233634.07770316866756e-050.00074349029544775
JUND#372746.994663941871030.000417684217818580.00391865990161289
MAX#414946.452555509007120.0005767613195645490.00485620569606594
MXI1#460149.96157162875930.0001015224754950450.00142473875547258
MYC#460945.22228187160940.001344309395272740.00888091143860392
NANOG#79923429.24477848101271.36586687657858e-065.33669175918409e-05
NFYA#4800418.42558069983058.67100748407158e-060.000234609158194029
NR2C2#7182432.61461090524098.82887529809196e-073.82288104169746e-05
NRF1#4899412.21027944771094.49717228915276e-050.000794183592673022
PAX5#507946.669565531177830.0005052774169483260.00444085400561021
REST#597849.650028716128020.0001152825614219170.00157118562342994
RFX5#5993412.04791082719514.74457429336527e-050.000827243062812647
RXRA#6256420.07461713913336.1537798808435e-060.000182376452036156
SIX5#147912417.0867153554591.17257016123224e-050.000297599161771406
SMARCB1#6598418.25271578115749.00423392720929e-060.000241622093300054
SP1#666745.69838137814090.0009482606065333980.00684607973771198
SPI1#668848.204323508522730.000220661881527680.00249547441741953
SRF#6722413.79717826216782.75840773062708e-050.000584707418264585
STAT1#6772420.70658749719925.43610708103893e-060.000165377683494502
STAT3#6774410.51946499715428.16377768286615e-050.00123174917281257
TAF1#687243.343046285745290.008005664898701650.0322434011937643
TAF7#6879411.43306940492395.85061525419808e-050.000969892708782846
TBP#690843.706770687096390.005296377814784350.0244399064462627
TCF7L2#6934410.77017656313737.42969445082454e-050.00115503104904683
TFAP2C#7022410.80922860986027.32289634782688e-050.0011457617553119
THAP1#55145431.36914460285131.03171810326891e-064.31870168285779e-05
TRIM28#10155418.59052504526258.36730015875654e-060.000230269423262286
USF1#739146.361499277207960.0006105011399140830.00508170308053614
USF2#7392412.99219738506963.50833029870167e-050.000681432970180591
YY1#752844.911170749853860.00171871838055440.0106903239203574
ZBTB7A#5134147.35190930787590.000342223540015990.00346802680921113
ZNF143#7702413.50087655222793.00867915035614e-050.000621240493839551
ZNF263#1012748.221841637010680.0002187871180958320.00249018175967857



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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