Personal tools

Coexpression cluster:C2491

From FANTOM5_SSTAR

Revision as of 15:14, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2491_placenta_chorionic_mesothelioma_choriocarcinoma_amniotic_Alveolar_rectal



Phase1 CAGE Peaks

Hg19::chr19:4233239..4233253,+p@chr19:4233239..4233253
+
Hg19::chr1:120049826..120049843,+p1@HSD3B1
Hg19::chr1:165864821..165864850,+p11@UCK2
Hg19::chr6:168720425..168720437,-p6@DACT2


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


GO IDGO nameFDR corrected p-value
GO:0004769steroid delta-isomerase activity0.00558016317052942
GO:0030868smooth endoplasmic reticulum membrane0.00558016317052942
GO:0004849uridine kinase activity0.00558016317052942
GO:0006702androgen biosynthetic process0.00558016317052942
GO:0006703estrogen biosynthetic process0.00558016317052942
GO:0008209androgen metabolic process0.00558016317052942
GO:00038543-beta-hydroxy-delta5-steroid dehydrogenase activity0.00558016317052942
GO:0006700C21-steroid hormone biosynthetic process0.00558016317052942
GO:0005790smooth endoplasmic reticulum0.00558016317052942
GO:0008210estrogen metabolic process0.00558016317052942
GO:0019206nucleoside kinase activity0.00591818063176459
GO:0008207C21-steroid hormone metabolic process0.00658720775069912
GO:0016863intramolecular oxidoreductase activity, transposing C



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><br><br>


Cell Type
Ontology termp-valuen
embryonic cell1.38e-07248
mesothelial cell2.01e-0719


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.