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Coexpression cluster:C3003

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Full id: C3003_mesothelioma_heart_basal_Fibroblast_Melanocyte_Mesenchymal_Retinal



Phase1 CAGE Peaks

Hg19::chr10:17659306..17659317,-p3@PTPLA
Hg19::chr10:17659325..17659355,-p1@PTPLA
Hg19::chr10:17659357..17659401,-p2@PTPLA


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
non-terminally differentiated cell1.26e-20180
embryonic cell3.68e-15248
epithelial cell3.66e-11254
fibroblast7.23e-1175
mesodermal cell2.19e-09119
animal cell1.62e-08679
eukaryotic cell1.62e-08679
mesothelial cell3.02e-0819
Uber Anatomy
Ontology termp-valuen
trunk5.77e-11216
trunk mesenchyme7.37e-11143
mesenchyme2.76e-10238
entire embryonic mesenchyme2.76e-10238
organism subdivision2.05e-09365
multi-tissue structure9.33e-09347
somite1.30e-0883
paraxial mesoderm1.30e-0883
presomitic mesoderm1.30e-0883
presumptive segmental plate1.30e-0883
trunk paraxial mesoderm1.30e-0883
presumptive paraxial mesoderm1.30e-0883
dermomyotome1.59e-0770
multilaminar epithelium3.62e-0782
surface structure9.01e-0795


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
CTCF#1066435.360256373075030.0064925092527670.0278148811982006
E2F1#186934.907389214879320.008460985347239390.0323364016789378
EGR1#195834.988179094810140.008056488137383440.0318885607739024
NFKB1#479035.488063424193840.006049381815655430.0268436177534516
RAD21#5885310.35503389545630.0009004912073565420.00661553187993176
SMC3#9126315.04493284493280.0002935825420371870.00307938807952413
ZBTB7A#5134137.35190930787590.002516255860282270.013955458859966



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.