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Coexpression cluster:C3203: Difference between revisions

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|full_id=C3203_testicular_Mast_H9_Eosinophils_iPS_immature_gall
|full_id=C3203_testicular_Mast_H9_Eosinophils_iPS_immature_gall
|id=C3203
|id=C3203
|ontology_enrichment_celltype=CL:0002319!4.80e-08!25
|ontology_enrichment_celltype=CL:0002319!4.48e-08!25;CL:0000039!8.52e-07!7;CL:0000586!8.52e-07!7
|ontology_enrichment_disease=DOID:0050687!1.99e-08!143;DOID:305!8.63e-08!106
|ontology_enrichment_disease=DOID:0050687!1.17e-09!143;DOID:305!8.68e-09!106
|ontology_enrichment_uberon=UBERON:0005743!5.13e-22!86;UBERON:0000073!2.28e-21!94;UBERON:0001016!2.28e-21!94;UBERON:0001017!4.33e-21!82;UBERON:0002346!6.28e-17!90;UBERON:0003075!7.67e-17!86;UBERON:0007284!7.67e-17!86;UBERON:0000955!1.22e-16!69;UBERON:0006238!1.22e-16!69;UBERON:0001049!1.46e-16!57;UBERON:0005068!1.46e-16!57;UBERON:0006241!1.46e-16!57;UBERON:0007135!1.46e-16!57;UBERON:0000924!2.19e-15!173;UBERON:0006601!2.19e-15!173;UBERON:0004121!3.97e-15!169;UBERON:0000062!1.29e-14!511;UBERON:0000033!1.70e-14!123;UBERON:0002616!2.98e-14!59;UBERON:0000153!3.11e-14!129;UBERON:0007811!3.11e-14!129;UBERON:0003056!5.19e-14!61;UBERON:0001893!9.66e-13!34;UBERON:0001869!1.39e-12!32;UBERON:0002780!1.51e-12!41;UBERON:0001890!1.51e-12!41;UBERON:0006240!1.51e-12!41;UBERON:0003080!2.30e-12!42;UBERON:0002020!2.47e-12!34;UBERON:0003528!2.47e-12!34;UBERON:0002791!2.68e-12!33;UBERON:0000922!6.49e-12!612;UBERON:0000956!1.71e-11!25;UBERON:0000203!1.71e-11!25;UBERON:0007023!1.47e-10!115;UBERON:0002619!1.97e-10!22;UBERON:0001950!4.60e-10!20;UBERON:0002050!1.20e-09!605;UBERON:0005423!1.20e-09!605;UBERON:0000923!1.29e-09!604;UBERON:0005291!1.29e-09!604;UBERON:0006598!1.29e-09!604;UBERON:0002532!1.29e-09!604;UBERON:0000064!3.50e-09!219
|ontology_enrichment_uberon=UBERON:0001017!4.13e-22!81;UBERON:0001016!1.26e-21!89;UBERON:0001049!1.93e-20!56;UBERON:0005068!1.93e-20!56;UBERON:0006241!1.93e-20!56;UBERON:0007135!1.93e-20!56;UBERON:0000073!1.64e-19!53;UBERON:0002616!1.64e-19!53;UBERON:0000955!5.34e-18!68;UBERON:0006238!5.34e-18!68;UBERON:0011216!5.74e-17!223;UBERON:0003075!1.40e-15!82;UBERON:0007284!1.40e-15!82;UBERON:0002346!4.18e-15!86;UBERON:0001893!1.10e-14!34;UBERON:0002780!1.29e-14!41;UBERON:0001890!1.29e-14!41;UBERON:0003080!1.29e-14!41;UBERON:0006240!1.29e-14!41;UBERON:0001869!3.42e-14!32;UBERON:0003528!3.46e-14!34;UBERON:0002020!3.46e-14!34;UBERON:0002791!1.13e-13!32;UBERON:0003056!3.37e-13!61;UBERON:0000956!5.93e-13!25;UBERON:0000203!5.93e-13!25;UBERON:0010371!6.11e-13!104;UBERON:0002619!4.13e-12!22;UBERON:0004121!5.52e-12!171;UBERON:0000924!5.52e-12!171;UBERON:0006601!5.52e-12!171;UBERON:0000062!7.64e-12!503;UBERON:0001950!2.41e-11!20;UBERON:0000922!8.16e-09!592;UBERON:0007023!1.31e-08!114;UBERON:0000064!4.21e-08!218;UBERON:0003076!4.03e-07!15;UBERON:0003057!4.03e-07!15;UBERON:0005423!9.00e-07!581;UBERON:0005409!9.36e-07!25;UBERON:0010314!9.82e-07!132
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129292724058445!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189286058182059!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0114973580475816!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278480091112462!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171234592609873!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320684273874976!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319260696103278!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460312022632643!FOSL2#2355;2:11.2868004030411:0.010053458697312:0.0376590930342729!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108380259849366!IRF4#3662;3:21.9145126867441:9.49854535978121e-05:0.00136172763051502!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443157071660711!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156233142749437!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.0324758616341029!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293358632128724!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268698757047267!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00662112089588214!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275586115179127!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308155448319816!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189615908658761!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139688112364864!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242110776453451!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0108972479145212
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}}
}}

Revision as of 14:53, 19 October 2012


Full id: C3203_testicular_Mast_H9_Eosinophils_iPS_immature_gall



Phase1 CAGE Peaks

Hg19::chr11:77184963..77185028,-p2@PAK1
Hg19::chr11:77185029..77185043,-p9@PAK1
Hg19::chr11:77185057..77185070,-p13@PAK1


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>

Cell Type
Ontology termp-valuen
neural cell4.48e-0825
germ line cell8.52e-077
germ cell8.52e-077
Uber Anatomy
Ontology termp-valuen
central nervous system4.13e-2281
nervous system1.26e-2189
neural tube1.93e-2056
neural rod1.93e-2056
future spinal cord1.93e-2056
neural keel1.93e-2056
regional part of nervous system1.64e-1953
regional part of brain1.64e-1953
brain5.34e-1868
future brain5.34e-1868
organ system subdivision5.74e-17223
neural plate1.40e-1582
presumptive neural plate1.40e-1582
neurectoderm4.18e-1586
telencephalon1.10e-1434
regional part of forebrain1.29e-1441
forebrain1.29e-1441
anterior neural tube1.29e-1441
future forebrain1.29e-1441
cerebral hemisphere3.42e-1432
brain grey matter3.46e-1434
gray matter3.46e-1434
regional part of telencephalon1.13e-1332
pre-chordal neural plate3.37e-1361
cerebral cortex5.93e-1325
pallium5.93e-1325
ecto-epithelium6.11e-13104
regional part of cerebral cortex4.13e-1222
ectoderm-derived structure5.52e-12171
ectoderm5.52e-12171
presumptive ectoderm5.52e-12171
organ7.64e-12503
neocortex2.41e-1120
embryo8.16e-09592
adult organism1.31e-08114
organ part4.21e-08218
posterior neural tube4.03e-0715
chordal neural plate4.03e-0715
developing anatomical structure9.00e-07581
gastrointestinal system9.36e-0725
structure with developmental contribution from neural crest9.82e-07132
Disease
Ontology termp-valuen
cell type cancer1.17e-09143
carcinoma8.68e-09106


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#467322.46317452600878.81932387510763e-050.00129292724058445
CCNT2#90536.336201576962630.003930750035764890.0189286058182059
CEBPB#105137.971147625824820.001974187055288560.0114973580475816
CTCF#1066435.360256373075030.0064925092527670.0278480091112462
CTCFL#140690319.74647435897440.0001298372005551160.00171234592609873
E2F6#187635.017155731697390.00791769806886330.0320684273874976
EGR1#195834.988179094810140.008056488137383440.0319260696103278
ELF1#199734.258097958807540.01295179875054610.0460312022632643
FOSL2#2355211.28680040304110.0100534586973120.0376590930342729
HMGN3#932438.178547723350590.001827766942164210.0108380259849366
IRF4#3662321.91451268674419.49854535978121e-050.00136172763051502
JUN#3725312.51282919233630.0005103313992726250.00443157071660711
JUND#372736.994663941871030.002921845042734990.0156233142749437
MEF2A#4205212.4954872730960.008235029478029740.0324758616341029
MYC#460935.22228187160940.007020843755740150.0293358632128724
NFKB1#479035.488063424193840.006049381815655430.0268698757047267
RAD21#5885310.35503389545630.0009004912073565420.00662112089588214
SIN3A#2594235.408884726815140.006318961977991520.0275586115179127
SMC3#9126315.04493284493280.0002935825420371870.00308155448319816
USF1#739136.361499277207960.00388404057290560.0189615908658761
ZBTB7A#5134137.35190930787590.002516255860282270.0139688112364864
ZEB1#6935316.88843201754390.0002075486917327580.00242110776453451
ZNF263#1012738.221841637010680.001799043925565870.0108972479145212



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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