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Coexpression cluster:C851: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!1.99e-27!83;UBERON:0002329!1.99e-27!83;UBERON:0003077!1.99e-27!83;UBERON:0003059!1.99e-27!83;UBERON:0007282!1.99e-27!83;UBERON:0009618!1.99e-27!83;UBERON:0007285!1.99e-27!83;UBERON:0004290!2.37e-23!70;UBERON:0000475!4.72e-19!365;UBERON:0001134!7.93e-19!61;UBERON:0002036!7.93e-19!61;UBERON:0003082!7.93e-19!61;UBERON:0002385!1.14e-18!63;UBERON:0001015!1.14e-18!63;UBERON:0000383!1.14e-18!63;UBERON:0000486!3.91e-18!82;UBERON:0000468!3.07e-13!659;UBERON:0000481!3.99e-13!347;UBERON:0003102!1.22e-12!95;UBERON:0004872!2.20e-12!84;UBERON:0005256!2.64e-11!143;UBERON:0002199!3.09e-10!45;UBERON:0002416!3.09e-10!45;UBERON:0001637!5.08e-10!42;UBERON:0003509!5.08e-10!42;UBERON:0004572!5.08e-10!42;UBERON:0000119!1.59e-09!312;UBERON:0000479!2.87e-09!787;UBERON:0004573!3.20e-09!33;UBERON:0004571!3.20e-09!33;UBERON:0000467!4.00e-09!625;UBERON:0007100!6.02e-09!27;UBERON:0000480!6.15e-09!626;UBERON:0000483!7.65e-09!309;UBERON:0000477!9.31e-09!286;UBERON:0007023!1.21e-08!115;UBERON:0000948!1.49e-08!24;UBERON:0005498!1.49e-08!24;UBERON:0004140!1.49e-08!24;UBERON:0009881!1.49e-08!24;UBERON:0004141!1.49e-08!24;UBERON:0003084!1.49e-08!24;UBERON:0007005!1.49e-08!24;UBERON:0004139!1.49e-08!24;UBERON:0004291!1.49e-08!24;UBERON:0002097!1.65e-08!40;UBERON:0001981!1.81e-08!60;UBERON:0007500!1.81e-08!60;UBERON:0004537!1.81e-08!60;UBERON:0006965!1.81e-08!60;UBERON:0002049!1.04e-07!79;UBERON:0007798!1.04e-07!79;UBERON:0000153!1.24e-07!129;UBERON:0007811!1.24e-07!129;UBERON:0000033!1.33e-07!123;UBERON:0004121!1.66e-07!169;UBERON:0002100!1.97e-07!216;UBERON:0000924!2.24e-07!173;UBERON:0006601!2.24e-07!173;UBERON:0001013!2.58e-07!14;UBERON:0001009!7.23e-07!113
|ontology_enrichment_uberon=UBERON:0000914!1.99e-27!83;UBERON:0002329!1.99e-27!83;UBERON:0003077!1.99e-27!83;UBERON:0003059!1.99e-27!83;UBERON:0007282!1.99e-27!83;UBERON:0009618!1.99e-27!83;UBERON:0007285!1.99e-27!83;UBERON:0004290!2.37e-23!70;UBERON:0000475!4.72e-19!365;UBERON:0001134!7.93e-19!61;UBERON:0002036!7.93e-19!61;UBERON:0003082!7.93e-19!61;UBERON:0002385!1.14e-18!63;UBERON:0001015!1.14e-18!63;UBERON:0000383!1.14e-18!63;UBERON:0000486!3.91e-18!82;UBERON:0000468!3.07e-13!659;UBERON:0000481!3.99e-13!347;UBERON:0003102!1.22e-12!95;UBERON:0004872!2.20e-12!84;UBERON:0005256!2.64e-11!143;UBERON:0002199!3.09e-10!45;UBERON:0002416!3.09e-10!45;UBERON:0001637!5.08e-10!42;UBERON:0003509!5.08e-10!42;UBERON:0004572!5.08e-10!42;UBERON:0000119!1.59e-09!312;UBERON:0000479!2.87e-09!787;UBERON:0004573!3.20e-09!33;UBERON:0004571!3.20e-09!33;UBERON:0000467!4.00e-09!625;UBERON:0007100!6.02e-09!27;UBERON:0000480!6.15e-09!626;UBERON:0000483!7.65e-09!309;UBERON:0000477!9.31e-09!286;UBERON:0007023!1.21e-08!115;UBERON:0000948!1.49e-08!24;UBERON:0005498!1.49e-08!24;UBERON:0004140!1.49e-08!24;UBERON:0009881!1.49e-08!24;UBERON:0004141!1.49e-08!24;UBERON:0003084!1.49e-08!24;UBERON:0007005!1.49e-08!24;UBERON:0004139!1.49e-08!24;UBERON:0004291!1.49e-08!24;UBERON:0002097!1.65e-08!40;UBERON:0001981!1.81e-08!60;UBERON:0007500!1.81e-08!60;UBERON:0004537!1.81e-08!60;UBERON:0006965!1.81e-08!60;UBERON:0002049!1.04e-07!79;UBERON:0007798!1.04e-07!79;UBERON:0000153!1.24e-07!129;UBERON:0007811!1.24e-07!129;UBERON:0000033!1.33e-07!123;UBERON:0004121!1.66e-07!169;UBERON:0002100!1.97e-07!216;UBERON:0000924!2.24e-07!173;UBERON:0006601!2.24e-07!173;UBERON:0001013!2.58e-07!14;UBERON:0001009!7.23e-07!113
|tf_chipseq_enrich=EP300#2033;7:4.74175920835624:0.000121144534944293:0.00164186531080288!SUZ12#23512;3:15.0347342733189:0.000857529598312641:0.00645427599583265
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}}
}}

Revision as of 12:03, 5 September 2012


Full id: C851_Fibroblast_mesenchymal_Myoblast_normal_Olfactory_skeletal_Osteoblast



Phase1 CAGE Peaks

Hg19::chr1:170632867..170632878,+p21@PRRX1
Hg19::chr1:170632907..170632916,+p22@PRRX1
Hg19::chr1:170632959..170632987,+p4@PRRX1
Hg19::chr1:170633225..170633230,+p25@PRRX1
Hg19::chr1:170633245..170633256,+p14@PRRX1
Hg19::chr1:170633262..170633285,+p3@PRRX1
Hg19::chr1:170633294..170633303,+p23@PRRX1
Hg19::chr1:170633348..170633399,+p2@PRRX1
Hg19::chr1:170633410..170633422,+p2@M95929
Hg19::chr1:170633459..170633473,+p1@M95929


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
somite1.99e-2783
paraxial mesoderm1.99e-2783
presomitic mesoderm1.99e-2783
presumptive segmental plate1.99e-2783
trunk paraxial mesoderm1.99e-2783
presumptive paraxial mesoderm1.99e-2783
dermomyotome2.37e-2370
organism subdivision4.72e-19365
skeletal muscle tissue7.93e-1961
striated muscle tissue7.93e-1961
myotome7.93e-1961
muscle tissue1.14e-1863
musculature1.14e-1863
musculature of body1.14e-1863
multilaminar epithelium3.91e-1882
multi-cellular organism3.07e-13659
multi-tissue structure3.99e-13347
surface structure1.22e-1295
splanchnic layer of lateral plate mesoderm2.20e-1284
trunk mesenchyme2.64e-11143
integument3.09e-1045
integumental system3.09e-1045
artery5.08e-1042
arterial blood vessel5.08e-1042
arterial system5.08e-1042
cell layer1.59e-09312
tissue2.87e-09787
systemic artery3.20e-0933
systemic arterial system3.20e-0933
anatomical system4.00e-09625
primary circulatory organ6.02e-0927
anatomical group6.15e-09626
epithelium7.65e-09309
anatomical cluster9.31e-09286
adult organism1.21e-08115
heart1.49e-0824
primitive heart tube1.49e-0824
primary heart field1.49e-0824
anterior lateral plate mesoderm1.49e-0824
heart tube1.49e-0824
heart primordium1.49e-0824
cardiac mesoderm1.49e-0824
cardiogenic plate1.49e-0824
heart rudiment1.49e-0824
skin of body1.65e-0840
blood vessel1.81e-0860
epithelial tube open at both ends1.81e-0860
blood vasculature1.81e-0860
vascular cord1.81e-0860
vasculature1.04e-0779
vascular system1.04e-0779
anterior region of body1.24e-07129
craniocervical region1.24e-07129
head1.33e-07123
ectoderm-derived structure1.66e-07169
trunk1.97e-07216
ectoderm2.24e-07173
presumptive ectoderm2.24e-07173
adipose tissue2.58e-0714
circulatory system7.23e-07113


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
EP300#203374.741759208356240.0001211445349442930.00164186531080288
SUZ12#23512315.03473427331890.0008575295983126410.00645427599583265



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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