Personal tools

Coexpression cluster:C504

From FANTOM5_SSTAR

Revision as of 14:54, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C504_leiomyoma_Lens_Ciliary_mesenchymal_Smooth_Mesothelial_Renal



Phase1 CAGE Peaks

Hg19::chr3:98515870..98515887,-p2@DCBLD2
Hg19::chr3:98515943..98515954,-p15@DCBLD2
Hg19::chr3:98516110..98516123,-p5@DCBLD2
Hg19::chr3:98516909..98516965,-p6@DCBLD2
Hg19::chr3:98516991..98517004,-p22@DCBLD2
Hg19::chr3:98517010..98517033,-p14@DCBLD2
Hg19::chr3:98517248..98517268,-p27@DCBLD2
Hg19::chr3:98517295..98517325,-p11@DCBLD2
Hg19::chr3:98517628..98517642,-p10@DCBLD2
Hg19::chr3:98517866..98517882,-p26@DCBLD2
Hg19::chr3:98518027..98518049,-p9@DCBLD2
Hg19::chr3:98518144..98518166,-p7@DCBLD2
Hg19::chr3:98518582..98518608,-p@chr3:98518582..98518608
-
Hg19::chr3:98518647..98518667,-p@chr3:98518647..98518667
-
Hg19::chr3:98530363..98530400,-p@chr3:98530363..98530400
-
Hg19::chr3:98531239..98531265,-p12@DCBLD2
Hg19::chr3:98531283..98531302,-p20@DCBLD2
Hg19::chr3:98536685..98536713,-p8@DCBLD2
Hg19::chr3:98536722..98536741,-p19@DCBLD2


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
trunk mesenchyme1.43e-21143
organism subdivision3.44e-19365
multilaminar epithelium4.64e-1982
cell layer3.67e-18312
epithelium3.70e-18309
trunk1.58e-17216
somite1.21e-1683
paraxial mesoderm1.21e-1683
presomitic mesoderm1.21e-1683
presumptive segmental plate1.21e-1683
trunk paraxial mesoderm1.21e-1683
presumptive paraxial mesoderm1.21e-1683
dermomyotome4.20e-1670
multi-tissue structure1.13e-15347
skeletal muscle tissue2.38e-1561
striated muscle tissue2.38e-1561
myotome2.38e-1561
unilaminar epithelium5.98e-15138
mesenchyme1.29e-14238
entire embryonic mesenchyme1.29e-14238
muscle tissue1.54e-1463
musculature1.54e-1463
musculature of body1.54e-1463
epithelial tube3.64e-14118
multi-cellular organism5.62e-13659
artery8.21e-1242
arterial blood vessel8.21e-1242
arterial system8.21e-1242
anatomical system1.50e-10625
anatomical group2.30e-10626
systemic artery9.77e-1033
systemic arterial system9.77e-1033
vasculature1.02e-0979
vascular system1.02e-0979
embryo1.31e-09612
primordium2.41e-09168
embryonic structure4.58e-09605
developing anatomical structure4.58e-09605
germ layer6.59e-09604
embryonic tissue6.59e-09604
presumptive structure6.59e-09604
epiblast (generic)6.59e-09604
anatomical cluster1.02e-08286
blood vessel2.72e-0860
epithelial tube open at both ends2.72e-0860
blood vasculature2.72e-0860
vascular cord2.72e-0860
splanchnic layer of lateral plate mesoderm2.92e-0884
surface structure5.87e-0895
anatomical conduit1.94e-07241
vessel2.20e-0769
pigment epithelium of eye4.07e-0711
Disease
Ontology termp-valuen
female reproductive organ cancer1.33e-0827
ovarian cancer1.52e-0814
reproductive organ cancer1.59e-0829


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


No analysis results for this cluster

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.