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Coexpression cluster:C3888

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Full id: C3888_Alveolar_Whole_Neutrophils_Eosinophils_mesothelioma_Renal_Bronchial



Phase1 CAGE Peaks

Hg19::chr1:159895266..159895275,-p2@TAGLN2
Hg19::chr1:159895286..159895305,-p1@CCDC19
p1@TAGLN2
Hg19::chr8:107710288..107710306,-p1@TAGLN2P1


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>


Cell Type
Ontology termp-valuen
animal cell8.97e-39679
eukaryotic cell8.97e-39679
native cell5.07e-38722
somatic cell5.05e-35588
mesodermal cell1.79e-14121
somatic stem cell1.81e-10433
embryonic cell4.23e-10250
stem cell9.09e-10441
squamous epithelial cell9.86e-1063
multi fate stem cell1.04e-09427
lining cell2.35e-0958
barrier cell2.35e-0958
epithelial cell6.36e-09253
classical monocyte8.47e-0842
CD14-positive, CD16-negative classical monocyte8.47e-0842
epithelial cell of nephron2.07e-0715
kidney cell3.25e-0717
kidney epithelial cell3.25e-0717
vascular associated smooth muscle cell4.21e-0732
leukocyte6.37e-07136
smooth muscle cell7.35e-0743
smooth muscle myoblast7.35e-0743
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm4.02e-20203
cardiovascular system2.72e-14109
mesoderm1.43e-13315
mesoderm-derived structure1.43e-13315
presumptive mesoderm1.43e-13315
circulatory system2.38e-13112
vessel4.70e-1268
splanchnic layer of lateral plate mesoderm9.46e-1283
epithelial tube open at both ends1.79e-1159
blood vessel1.79e-1159
blood vasculature1.79e-1159
vascular cord1.79e-1159
artery5.76e-1142
arterial blood vessel5.76e-1142
arterial system5.76e-1142
epithelial tube7.35e-11117
vasculature1.26e-1078
vascular system1.26e-1078
nephron epithelium2.07e-0715
renal tubule2.07e-0715
nephron tubule2.07e-0715
nephron2.07e-0715
uriniferous tubule2.07e-0715
nephrogenic mesenchyme2.07e-0715
systemic artery4.64e-0733
systemic arterial system4.64e-0733


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
ESR1#2099220.51240219743630.003099741577095180.0163106565180493
GTF2B#2959221.29588662288280.002878180589911410.0155821005976755
IRF4#3662214.60967512449610.006056122473217890.0268381794450038
SMARCB1#6598212.16847718743830.008675002221921740.0329901524616861
TRIM28#10155212.39368336350830.008368344129438470.0329121254955535



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.