Personal tools

Coexpression cluster:C1625

From FANTOM5_SSTAR

Revision as of 17:29, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1625_Olfactory_basal_Ewing_Adipocyte_mesenchymal_Smooth_serous



Phase1 CAGE Peaks

Hg19::chr11:18418371..18418411,+p4@LDHA
Hg19::chr11:18422386..18422436,+p1@BC011633
Hg19::chr11:18428943..18428962,+p@chr11:18428943..18428962
+
Hg19::chr11:18429000..18429101,+p@chr11:18429000..18429101
+
Hg19::chr11:18429207..18429235,+p@chr11:18429207..18429235
+


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:0004459L-lactate dehydrogenase activity0.00333608069390478
GO:0019642anaerobic glycolysis0.00333608069390478
GO:0004457lactate dehydrogenase activity0.00333608069390478
GO:0006100tricarboxylic acid cycle intermediate metabolic process0.00800659366537148
GO:0006096glycolysis0.0137255891406368
GO:0006007glucose catabolic process0.0137255891406368
GO:0019320hexose catabolic process0.0137255891406368
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0137255891406368
GO:0046365monosaccharide catabolic process0.0137255891406368
GO:0046164alcohol catabolic process0.0137255891406368
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0137255891406368
GO:0044275cellular carbohydrate catabolic process0.0137255891406368
GO:0016052carbohydrate catabolic process0.0137255891406368
GO:0006006glucose metabolic process0.0137255891406368
GO:0019318hexose metabolic process0.0171391145649358
GO:0005996monosaccharide metabolic process0.0171391145649358
GO:0006066alcohol metabolic process0.0261980454491934
GO:0044262cellular carbohydrate metabolic process0.0275490032038769
GO:0044265cellular macromolecule catabolic process0.0275490032038769
GO:0005829cytosol0.0284234075120688
GO:0009057macromolecule catabolic process0.029786434767007
GO:0005975carbohydrate metabolic process0.03520290367003
GO:0044248cellular catabolic process0.03520290367003
GO:0009056catabolic process0.0405750814396169



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
non-terminally differentiated cell5.29e-14180
fibroblast8.80e-0875
animal cell5.53e-07679
eukaryotic cell5.53e-07679
Uber Anatomy
Ontology termp-valuen
multilaminar epithelium1.23e-0782
dermomyotome1.47e-0770
somite2.14e-0783
paraxial mesoderm2.14e-0783
presomitic mesoderm2.14e-0783
presumptive segmental plate2.14e-0783
trunk paraxial mesoderm2.14e-0783
presumptive paraxial mesoderm2.14e-0783
larynx3.97e-079
Disease
Ontology termp-valuen
disease of cellular proliferation1.20e-08239
cancer1.45e-08235


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.