Personal tools

Coexpression cluster:C3895

From FANTOM5_SSTAR

Revision as of 16:25, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3895_mature_Preadipocyte_extraskeletal_Fibroblast_adipose_Adipocyte_Olfactory



Phase1 CAGE Peaks

Hg19::chr1:162602303..162602315,+p4@DDR2
Hg19::chr1:162602328..162602360,+p3@DDR2
Hg19::chr5:32712363..32712425,+p7@NPR3


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:0016941natriuretic peptide receptor activity0.00565171317555634
GO:0017046peptide hormone binding0.0254297146523079
GO:0007193G-protein signaling, adenylate cyclase inhibiting pathway0.0339017942465337
GO:0042562hormone binding0.0367226181792955
GO:0008217regulation of blood pressure0.0392242564109015
GO:0043168anion binding0.0392242564109015
GO:0031404chloride ion binding0.0392242564109015
GO:0004888transmembrane receptor activity0.0392242564109015
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0392242564109015
GO:0019933cAMP-mediated signaling0.0392242564109015
GO:0007166cell surface receptor linked signal transduction0.0392242564109015
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0392242564109015
GO:0004714transmembrane receptor protein tyrosine kinase activity0.0392242564109015
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0392242564109015
GO:0019935cyclic-nucleotide-mediated signaling0.0392242564109015
GO:0019199transmembrane receptor protein kinase activity0.0392242564109015
GO:0048015phosphoinositide-mediated signaling0.0392242564109015
GO:0004872receptor activity0.0392242564109015
GO:0001653peptide receptor activity0.0392242564109015
GO:0008528peptide receptor activity, G-protein coupled0.0392242564109015
GO:0042803protein homodimerization activity0.0392242564109015
GO:0008015blood circulation0.0392242564109015
GO:0003013circulatory system process0.0392242564109015
GO:0060089molecular transducer activity0.0422574573003398
GO:0004871signal transducer activity0.0422574573003398
GO:0042277peptide binding0.0422574573003398
GO:0001501skeletal development0.0422574573003398
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0422574573003398
GO:0008284positive regulation of cell proliferation0.0452535363805448



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><br>


Uber Anatomy
Ontology termp-valuen
muscle tissue4.02e-1264
musculature4.02e-1264
musculature of body4.02e-1264
dense mesenchyme tissue4.43e-1273
somite5.58e-1271
presomitic mesoderm5.58e-1271
presumptive segmental plate5.58e-1271
dermomyotome5.58e-1271
trunk paraxial mesoderm5.58e-1271
skeletal muscle tissue8.21e-1262
striated muscle tissue8.21e-1262
myotome8.21e-1262
paraxial mesoderm1.50e-1172
presumptive paraxial mesoderm1.50e-1172
multilaminar epithelium1.06e-0983
epithelial vesicle2.78e-0978
trunk mesenchyme2.57e-07122
mesenchyme2.78e-07160
entire embryonic mesenchyme2.78e-07160
integument4.36e-0746
integumental system4.36e-0746
surface structure8.96e-0799


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.