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Coexpression cluster:C2074: Difference between revisions

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|tf_chipseq_enrich=TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321109008508911
|tf_chipseq_enrich=TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321109008508911
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}}
}}

Revision as of 15:16, 26 November 2012


Full id: C2074_Mesenchymal_Osteoblast_Adipocyte_mature_Chondrocyte_Synoviocyte_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr10:81892415..81892447,+p2@PLAC9
Hg19::chr10:81892478..81892493,+p1@PLAC9
Hg19::chr5:158527633..158527660,+p1@ENST00000523301
Hg19::chr5:158527667..158527701,+p1@ENST00000499583
p1@uc003lxm.1


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
dense mesenchyme tissue1.45e-2073
somite2.87e-2071
presomitic mesoderm2.87e-2071
presumptive segmental plate2.87e-2071
dermomyotome2.87e-2071
trunk paraxial mesoderm2.87e-2071
paraxial mesoderm3.31e-2072
presumptive paraxial mesoderm3.31e-2072
muscle tissue4.48e-1864
musculature4.48e-1864
musculature of body4.48e-1864
skeletal muscle tissue1.71e-1762
striated muscle tissue1.71e-1762
myotome1.71e-1762
epithelial vesicle2.14e-1778
multilaminar epithelium5.58e-1683
splanchnic layer of lateral plate mesoderm2.14e-1483
multi-tissue structure1.01e-13342
structure with developmental contribution from neural crest1.64e-12132
trunk mesenchyme5.70e-12122
mesenchyme2.38e-11160
entire embryonic mesenchyme2.38e-11160
cell layer4.62e-11309
adult organism4.70e-11114
epithelium1.42e-10306
circulatory system1.62e-10112
primary circulatory organ2.11e-1027
multi-cellular organism2.37e-10656
vasculature2.91e-1078
vascular system2.91e-1078
cardiovascular system7.98e-10109
anatomical cluster9.01e-10373
organism subdivision1.04e-09264
adipose tissue1.30e-0914
heart1.31e-0924
primitive heart tube1.31e-0924
primary heart field1.31e-0924
anterior lateral plate mesoderm1.31e-0924
heart tube1.31e-0924
heart primordium1.31e-0924
cardiac mesoderm1.31e-0924
cardiogenic plate1.31e-0924
heart rudiment1.31e-0924
epithelial tube open at both ends2.73e-0959
blood vessel2.73e-0959
blood vasculature2.73e-0959
vascular cord2.73e-0959
unilaminar epithelium3.71e-09148
artery4.55e-0942
arterial blood vessel4.55e-0942
arterial system4.55e-0942
tissue4.20e-08773
vessel5.48e-0868
anatomical conduit8.21e-08240
systemic artery8.89e-0833
systemic arterial system8.89e-0833
surface structure1.19e-0799
trunk8.37e-07199
anatomical system9.43e-07624


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
TAF1#687243.343046285745290.008005664898701650.0321109008508911



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.