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Coexpression cluster:C3622

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Full id: C3622_Mesenchymal_Alveolar_Renal_Smooth_Osteoblast_Keratocytes_Hair



Phase1 CAGE Peaks

Hg19::chr17:27044810..27044873,-p2@RAB34
Hg19::chr17:27044878..27044894,-p3@RAB34
Hg19::chr17:27045165..27045230,-p1@RAB34


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
multilaminar epithelium1.42e-2283
epithelial vesicle4.12e-2278
somite1.47e-2071
presomitic mesoderm1.47e-2071
presumptive segmental plate1.47e-2071
dermomyotome1.47e-2071
trunk paraxial mesoderm1.47e-2071
dense mesenchyme tissue2.13e-2073
paraxial mesoderm5.35e-2072
presumptive paraxial mesoderm5.35e-2072
organism subdivision2.42e-18264
mesenchyme8.63e-18160
entire embryonic mesenchyme8.63e-18160
skeletal muscle tissue8.53e-1762
striated muscle tissue8.53e-1762
myotome8.53e-1762
muscle tissue2.63e-1664
musculature2.63e-1664
musculature of body2.63e-1664
trunk7.03e-16199
trunk mesenchyme1.99e-14122
multi-tissue structure4.33e-13342
surface structure4.62e-1299
multi-cellular organism1.02e-10656
unilaminar epithelium1.40e-10148
splanchnic layer of lateral plate mesoderm5.44e-1083
epithelial tube9.11e-10117
cell layer1.15e-09309
epithelium1.75e-09306
artery2.94e-0942
arterial blood vessel2.94e-0942
arterial system2.94e-0942
anatomical system3.02e-09624
anatomical group5.79e-09625
vasculature6.69e-0978
vascular system6.69e-0978
integument8.84e-0946
integumental system8.84e-0946
epithelial tube open at both ends5.30e-0859
blood vessel5.30e-0859
blood vasculature5.30e-0859
vascular cord5.30e-0859
systemic artery9.05e-0833
systemic arterial system9.05e-0833
skin of body1.38e-0741
embryo1.55e-07592
developing anatomical structure1.68e-07581
compound organ1.98e-0768
urinary system structure5.15e-0747
anatomical cluster6.17e-07373
renal system7.09e-0748
organ component layer7.74e-0766
vessel9.38e-0768


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
FOS#235338.99795530889440.001372499272417130.00896674912498264
JUND#372736.994663941871030.002921845042734990.0156561784627879
SMARCB1#6598212.16847718743830.008675002221921740.0329817457974257
SMARCC1#6599343.66335931963151.20046018043203e-050.000301599376435268
SMARCC2#6601394.15537442689761.19621075407887e-064.85169145418419e-05
STAT3#6774310.51946499715420.0008589184530415310.00642352913119975



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.