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Coexpression cluster:C3050

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Full id: C3050_teratocarcinoma_breast_seminal_neuroblastoma_MCF7_kidney_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr10:8087114..8087132,+p@chr10:8087114..8087132
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Hg19::chr10:8087281..8087303,+p@chr10:8087281..8087303
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Hg19::chr10:8087309..8087356,+p@chr10:8087309..8087356
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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>


Cell Type
Ontology termp-valuen
epithelial cell7.86e-12253
transitional epithelial cell9.06e-084
urothelial cell9.06e-084
Uber Anatomy
Ontology termp-valuen
renal system4.16e-1848
urinary system structure5.94e-1747
extraembryonic membrane5.34e-1114
membranous layer5.34e-1114
urothelium2.68e-095
chorion4.28e-097
placenta5.71e-084
allantois5.71e-084
internal genitalia6.57e-0825
transitional epithelium1.18e-076
male genital duct6.06e-073
internal male genitalia6.06e-073
cavitated compound organ7.47e-0731
Disease
Ontology termp-valuen
cell type cancer1.04e-09143
cancer2.08e-09235
thoracic cancer5.27e-094
breast cancer5.27e-094
disease of cellular proliferation6.37e-09239


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
E2F1#186934.907389214879320.008460985347239390.0323482391434028
ELF1#199734.258097958807540.01295179875054610.0459952024791147
EP300#203336.77394172622320.003216880500103790.0166816178028967
FOXA1#3169311.08141974938550.000734755275698670.00579322861533243
SP1#666735.69838137814090.005403962701712170.0245384548088747
SUZ12#23512350.11578091106297.93834897779404e-060.000221086194371155



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.