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Coexpression cluster:C2034

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Full id: C2034_mesenchymal_Synoviocyte_Fibroblast_Preadipocyte_Nucleus_Cardiac_Smooth



Phase1 CAGE Peaks

Hg19::chr10:111765588..111765603,+p8@ADD3
Hg19::chr10:111765636..111765647,+p14@ADD3
Hg19::chr10:111765684..111765732,+p3@ADD3
Hg19::chr10:111765736..111765747,+p12@ADD3


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
paraxial mesoderm3.19e-1972
presumptive paraxial mesoderm3.19e-1972
somite9.20e-1971
presomitic mesoderm9.20e-1971
presumptive segmental plate9.20e-1971
dermomyotome9.20e-1971
trunk paraxial mesoderm9.20e-1971
dense mesenchyme tissue1.39e-1873
adult organism4.37e-18114
muscle tissue7.34e-1864
musculature7.34e-1864
musculature of body7.34e-1864
multi-tissue structure2.10e-17342
skeletal muscle tissue3.73e-1762
striated muscle tissue3.73e-1762
myotome3.73e-1762
epithelial vesicle1.48e-1578
multilaminar epithelium2.95e-1583
mesenchyme3.56e-13160
entire embryonic mesenchyme3.56e-13160
structure with developmental contribution from neural crest1.09e-12132
trunk mesenchyme1.21e-12122
cell layer2.08e-11309
multi-cellular organism5.55e-11656
anatomical cluster9.35e-11373
epithelium9.55e-11306
anatomical system2.24e-09624
anatomical group3.20e-09625
tissue4.31e-09773
neural tube1.57e-0856
neural rod1.57e-0856
future spinal cord1.57e-0856
neural keel1.57e-0856
heart2.34e-0824
primitive heart tube2.34e-0824
primary heart field2.34e-0824
anterior lateral plate mesoderm2.34e-0824
heart tube2.34e-0824
heart primordium2.34e-0824
cardiac mesoderm2.34e-0824
cardiogenic plate2.34e-0824
heart rudiment2.34e-0824
brain2.87e-0868
future brain2.87e-0868
primary circulatory organ1.29e-0727
regional part of forebrain1.37e-0741
forebrain1.37e-0741
anterior neural tube1.37e-0741
future forebrain1.37e-0741
central nervous system1.65e-0781
regional part of nervous system1.67e-0753
regional part of brain1.67e-0753
anatomical conduit1.80e-07240
unilaminar epithelium7.07e-07148
germ layer7.51e-07560
germ layer / neural crest7.51e-07560
embryonic tissue7.51e-07560
presumptive structure7.51e-07560
germ layer / neural crest derived structure7.51e-07560
epiblast (generic)7.51e-07560
nervous system8.54e-0789
tube9.28e-07192
organ system subdivision9.68e-07223


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
CEBPB#105147.971147625824820.0002476385788090830.00267346759688255
FOXA1#3169411.08141974938556.62943068949433e-050.00106863885133523
TRIM28#10155418.59052504526258.36730015875654e-060.000229423066757778



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.