Personal tools

Coexpression cluster:C3833

From FANTOM5_SSTAR

Revision as of 17:39, 18 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3833_Dendritic_lymph_dura_CD14_duodenum_vein_left



Phase1 CAGE Peaks

Hg19::chr19:7805780..7805799,-p@chr19:7805780..7805799
-
Hg19::chr19:7807611..7807619,-p1@AK057212
Hg19::chr19:7812412..7812426,-p2@CD209


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:0046795intracellular virion transport0.0010891322265395
GO:0046794virion transport0.0010891322265395
GO:0046968peptide antigen transport0.0010891322265395
GO:0042607exogenous peptide antigen binding0.0010891322265395
GO:0019062virion attachment to host cell surface receptor0.0013069586718474
GO:0046790virion binding0.00140946523434524
GO:0007159leukocyte adhesion0.00140946523434524
GO:0044409entry into host0.00140946523434524
GO:0030260entry into host cell0.00140946523434524
GO:0046718entry of virus into host cell0.00140946523434524
GO:0007157heterophilic cell adhesion0.00140946523434524
GO:0052126movement in host environment0.00140946523434524
GO:0019048virus-host interaction0.00140946523434524
GO:0051828entry into other organism during symbiotic interaction0.00140946523434524
GO:0019059initiation of viral infection0.00140946523434524
GO:0051806entry into cell of other organism during symbiotic interaction0.00140946523434524
GO:0052192movement in environment of other organism during symbiotic interaction0.00140946523434524
GO:0005537mannose binding0.00145217630205267
GO:0009405pathogenesis0.00149039146789616
GO:0009988cell-cell recognition0.0015247851171553
GO:0048029monosaccharide binding0.00176335693820681
GO:0042605peptide antigen binding0.001782216370701
GO:0051701interaction with host0.00208355730294514
GO:0019079viral genome replication0.00263206954747047
GO:0044403symbiosis, encompassing mutualism through parasitism0.00268094086532801
GO:0044419interspecies interaction between organisms0.00268094086532801
GO:0008037cell recognition0.0030340112025029
GO:0015833peptide transport0.0030340112025029
GO:0019058viral infectious cycle0.0037556283673776
GO:0022415viral reproductive process0.00413870246085011
GO:0048002antigen processing and presentation of peptide antigen0.00737799250236437
GO:0003823antigen binding0.0120485252560932
GO:0010324membrane invagination0.012621120507546
GO:0006897endocytosis0.012621120507546
GO:0042277peptide binding0.0129451144640124
GO:0016044membrane organization and biogenesis0.0171840862409566
GO:0022414reproductive process0.0179559637348405
GO:0051704multi-organism process0.0188964441304604
GO:0016337cell-cell adhesion0.0188964441304604
GO:0005529sugar binding0.0188964441304604
GO:0019882antigen processing and presentation0.0220482865372631
GO:0030246carbohydrate binding0.0247907240136135
GO:0016192vesicle-mediated transport0.0306983315945553
GO:0046907intracellular transport0.0450504693704976
GO:0022610biological adhesion0.0454594320642575
GO:0007155cell adhesion0.0454594320642575



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

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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.