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Coexpression cluster:C4242: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!1.13e-21!365;UBERON:0000468!2.15e-19!659;UBERON:0000481!9.38e-18!347;UBERON:0000477!3.69e-16!286;UBERON:0000483!1.43e-15!309;UBERON:0000119!2.14e-15!312;UBERON:0002385!2.15e-15!63;UBERON:0001015!2.15e-15!63;UBERON:0000383!2.15e-15!63;UBERON:0001134!4.15e-15!61;UBERON:0002036!4.15e-15!61;UBERON:0003082!4.15e-15!61;UBERON:0004290!5.39e-15!70;UBERON:0000914!6.86e-14!83;UBERON:0002329!6.86e-14!83;UBERON:0003077!6.86e-14!83;UBERON:0003059!6.86e-14!83;UBERON:0007282!6.86e-14!83;UBERON:0009618!6.86e-14!83;UBERON:0007285!6.86e-14!83;UBERON:0004872!3.09e-13!84;UBERON:0000486!8.90e-13!82;UBERON:0000467!4.95e-12!625;UBERON:0000480!8.99e-12!626;UBERON:0004111!2.47e-11!241;UBERON:0002049!5.13e-11!79;UBERON:0007798!5.13e-11!79;UBERON:0005256!6.51e-11!143;UBERON:0000025!1.12e-10!194;UBERON:0002100!1.88e-10!216;UBERON:0001637!4.18e-10!42;UBERON:0003509!4.18e-10!42;UBERON:0004572!4.18e-10!42;UBERON:0001981!4.19e-10!60;UBERON:0007500!4.19e-10!60;UBERON:0004537!4.19e-10!60;UBERON:0006965!4.19e-10!60;UBERON:0000922!5.08e-10!612;UBERON:0002050!7.46e-10!605;UBERON:0005423!7.46e-10!605;UBERON:0000923!1.31e-09!604;UBERON:0005291!1.31e-09!604;UBERON:0006598!1.31e-09!604;UBERON:0002532!1.31e-09!604;UBERON:0003104!2.04e-09!238;UBERON:0009142!2.04e-09!238;UBERON:0004573!3.11e-09!33;UBERON:0004571!3.11e-09!33;UBERON:0000055!5.05e-09!69;UBERON:0000490!2.32e-08!138;UBERON:0004535!6.16e-08!110;UBERON:0001009!7.77e-08!113;UBERON:0003914!8.94e-08!118;UBERON:0000064!1.91e-07!219;UBERON:0002346!2.14e-07!90;UBERON:0000948!8.95e-07!24;UBERON:0005498!8.95e-07!24;UBERON:0004140!8.95e-07!24;UBERON:0009881!8.95e-07!24;UBERON:0004141!8.95e-07!24;UBERON:0003084!8.95e-07!24;UBERON:0007005!8.95e-07!24;UBERON:0004139!8.95e-07!24;UBERON:0004291!8.95e-07!24;UBERON:0000924!9.34e-07!173;UBERON:0006601!9.34e-07!173
|ontology_enrichment_uberon=UBERON:0000475!1.13e-21!365;UBERON:0000468!2.15e-19!659;UBERON:0000481!9.38e-18!347;UBERON:0000477!3.69e-16!286;UBERON:0000483!1.43e-15!309;UBERON:0000119!2.14e-15!312;UBERON:0002385!2.15e-15!63;UBERON:0001015!2.15e-15!63;UBERON:0000383!2.15e-15!63;UBERON:0001134!4.15e-15!61;UBERON:0002036!4.15e-15!61;UBERON:0003082!4.15e-15!61;UBERON:0004290!5.39e-15!70;UBERON:0000914!6.86e-14!83;UBERON:0002329!6.86e-14!83;UBERON:0003077!6.86e-14!83;UBERON:0003059!6.86e-14!83;UBERON:0007282!6.86e-14!83;UBERON:0009618!6.86e-14!83;UBERON:0007285!6.86e-14!83;UBERON:0004872!3.09e-13!84;UBERON:0000486!8.90e-13!82;UBERON:0000467!4.95e-12!625;UBERON:0000480!8.99e-12!626;UBERON:0004111!2.47e-11!241;UBERON:0002049!5.13e-11!79;UBERON:0007798!5.13e-11!79;UBERON:0005256!6.51e-11!143;UBERON:0000025!1.12e-10!194;UBERON:0002100!1.88e-10!216;UBERON:0001637!4.18e-10!42;UBERON:0003509!4.18e-10!42;UBERON:0004572!4.18e-10!42;UBERON:0001981!4.19e-10!60;UBERON:0007500!4.19e-10!60;UBERON:0004537!4.19e-10!60;UBERON:0006965!4.19e-10!60;UBERON:0000922!5.08e-10!612;UBERON:0002050!7.46e-10!605;UBERON:0005423!7.46e-10!605;UBERON:0000923!1.31e-09!604;UBERON:0005291!1.31e-09!604;UBERON:0006598!1.31e-09!604;UBERON:0002532!1.31e-09!604;UBERON:0003104!2.04e-09!238;UBERON:0009142!2.04e-09!238;UBERON:0004573!3.11e-09!33;UBERON:0004571!3.11e-09!33;UBERON:0000055!5.05e-09!69;UBERON:0000490!2.32e-08!138;UBERON:0004535!6.16e-08!110;UBERON:0001009!7.77e-08!113;UBERON:0003914!8.94e-08!118;UBERON:0000064!1.91e-07!219;UBERON:0002346!2.14e-07!90;UBERON:0000948!8.95e-07!24;UBERON:0005498!8.95e-07!24;UBERON:0004140!8.95e-07!24;UBERON:0009881!8.95e-07!24;UBERON:0004141!8.95e-07!24;UBERON:0003084!8.95e-07!24;UBERON:0007005!8.95e-07!24;UBERON:0004139!8.95e-07!24;UBERON:0004291!8.95e-07!24;UBERON:0000924!9.34e-07!173;UBERON:0006601!9.34e-07!173
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}}
}}

Revision as of 12:35, 5 September 2012


Full id: C4242_Myoblast_Preadipocyte_Chondrocyte_Mesenchymal_mesenchymal_mesothelioma_Adipocyte



Phase1 CAGE Peaks

Hg19::chr2:69240302..69240332,+p1@ANTXR1
Hg19::chr2:69240415..69240424,+p5@ANTXR1
Hg19::chr2:69240547..69240561,+p4@ANTXR1


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><br>

Uber Anatomy
Ontology termp-valuen
organism subdivision1.13e-21365
multi-cellular organism2.15e-19659
multi-tissue structure9.38e-18347
anatomical cluster3.69e-16286
epithelium1.43e-15309
cell layer2.14e-15312
muscle tissue2.15e-1563
musculature2.15e-1563
musculature of body2.15e-1563
skeletal muscle tissue4.15e-1561
striated muscle tissue4.15e-1561
myotome4.15e-1561
dermomyotome5.39e-1570
somite6.86e-1483
paraxial mesoderm6.86e-1483
presomitic mesoderm6.86e-1483
presumptive segmental plate6.86e-1483
trunk paraxial mesoderm6.86e-1483
presumptive paraxial mesoderm6.86e-1483
splanchnic layer of lateral plate mesoderm3.09e-1384
multilaminar epithelium8.90e-1382
anatomical system4.95e-12625
anatomical group8.99e-12626
anatomical conduit2.47e-11241
vasculature5.13e-1179
vascular system5.13e-1179
trunk mesenchyme6.51e-11143
tube1.12e-10194
trunk1.88e-10216
artery4.18e-1042
arterial blood vessel4.18e-1042
arterial system4.18e-1042
blood vessel4.19e-1060
epithelial tube open at both ends4.19e-1060
blood vasculature4.19e-1060
vascular cord4.19e-1060
embryo5.08e-10612
embryonic structure7.46e-10605
developing anatomical structure7.46e-10605
germ layer1.31e-09604
embryonic tissue1.31e-09604
presumptive structure1.31e-09604
epiblast (generic)1.31e-09604
mesenchyme2.04e-09238
entire embryonic mesenchyme2.04e-09238
systemic artery3.11e-0933
systemic arterial system3.11e-0933
vessel5.05e-0969
unilaminar epithelium2.32e-08138
cardiovascular system6.16e-08110
circulatory system7.77e-08113
epithelial tube8.94e-08118
organ part1.91e-07219
neurectoderm2.14e-0790
heart8.95e-0724
primitive heart tube8.95e-0724
primary heart field8.95e-0724
anterior lateral plate mesoderm8.95e-0724
heart tube8.95e-0724
heart primordium8.95e-0724
cardiac mesoderm8.95e-0724
cardiogenic plate8.95e-0724
heart rudiment8.95e-0724
ectoderm9.34e-07173
presumptive ectoderm9.34e-07173


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
CTCF#1066435.360256373075030.0064925092527670.0280298943346589
CTCFL#140690213.16431623931620.007433367036996010.0306899675828916
ELK4#2005316.2356816584680.0002336043955745990.00256087010280419
GABPB1#255337.067683836182170.002832212825417420.0154501684655926
HDAC2#3066313.41562023662630.0004140761399857210.00392357992959251
MAX#414936.452555509007120.003721913834265510.0187025095716347
NR2C2#7182332.61461090524092.88098172333076e-050.000605771794247919
RAD21#5885310.35503389545630.0009004912073565420.00665956671895694
SIX5#147912317.0867153554590.0002004060546325010.00240052849406627
SMC3#9126315.04493284493280.0002935825420371870.00309836975624714
YY1#752834.911170749853860.008441455341808260.0330255536408733
ZBTB7A#5134137.35190930787590.002516255860282270.0140562283799754



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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