Personal tools

Coexpression cluster:C2173

From FANTOM5_SSTAR

Revision as of 17:36, 18 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2173_CD14_Hepatocyte_liver_Monocytederived_Macrophage_myeloma_lung



Phase1 CAGE Peaks

Hg19::chr11:914812..914866,-p3@CHID1
Hg19::chr6:31895467..31895479,+p4@C2
p6@CFB
Hg19::chr6:31895480..31895530,+p1@C2
Hg19::chr7:150488653..150488682,-p@chr7:150488653..150488682
-


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:0003813classical-complement-pathway C3/C5 convertase activity0.00523960908983869
GO:0006032chitin catabolic process0.0112254201983592
GO:0006046N-acetylglucosamine catabolic process0.0112254201983592
GO:0006043glucosamine catabolic process0.0112254201983592
GO:0006030chitin metabolic process0.0112254201983592
GO:0004568chitinase activity0.0112254201983592
GO:0046348amino sugar catabolic process0.0112254201983592
GO:0044247cellular polysaccharide catabolic process0.0122221556631645
GO:0000272polysaccharide catabolic process0.0122221556631645
GO:0006958complement activation, classical pathway0.0134185936103104
GO:0002455humoral immune response mediated by circulating immunoglobulin0.0134185936103104
GO:0006044N-acetylglucosamine metabolic process0.0134185936103104
GO:0006041glucosamine metabolic process0.0134185936103104
GO:0006956complement activation0.0134185936103104
GO:0002541activation of plasma proteins during acute inflammatory response0.0134185936103104
GO:0006040amino sugar metabolic process0.0134185936103104
GO:0016064immunoglobulin mediated immune response0.0151252863041258
GO:0019724B cell mediated immunity0.0151252863041258
GO:0002253activation of immune response0.0155187118245836
GO:0002449lymphocyte mediated immunity0.0155187118245836
GO:0006959humoral immune response0.0155187118245836
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0155187118245836
GO:0002250adaptive immune response0.0155187118245836
GO:0002443leukocyte mediated immunity0.0155187118245836
GO:0002526acute inflammatory response0.0155187118245836
GO:0044264cellular polysaccharide metabolic process0.0155187118245836
GO:0050778positive regulation of immune response0.0155187118245836
GO:0005976polysaccharide metabolic process0.0155187118245836
GO:0002684positive regulation of immune system process0.0155187118245836
GO:0050776regulation of immune response0.0168773365271673
GO:0002682regulation of immune system process0.0168773365271673
GO:0051240positive regulation of multicellular organismal process0.0171661505175509
GO:0002252immune effector process0.017437343782983
GO:0045087innate immune response0.0175388820935643
GO:0044275cellular carbohydrate catabolic process0.0270582014484685
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.0270582014484685
GO:0016052carbohydrate catabolic process0.0270582014484685
GO:0005764lysosome0.0270582014484685
GO:0000323lytic vacuole0.0270582014484685
GO:0016798hydrolase activity, acting on glycosyl bonds0.0287249603360411
GO:0016787hydrolase activity0.0289680995531216
GO:0005773vacuole0.0289680995531216
GO:0051239regulation of multicellular organismal process0.0336157169153266
GO:0006954inflammatory response0.0345049587537292
GO:0004252serine-type endopeptidase activity0.0385836416675041
GO:0008236serine-type peptidase activity0.0417957633034446
GO:0017171serine hydrolase activity0.0417957633034446
GO:0009611response to wounding0.0458872597308855
GO:0043285biopolymer catabolic process0.0482229001898716
GO:0044260cellular macromolecule metabolic process0.0493324365086639



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.