journal.pone.0123678.pdf 1,63MB
1000 Titel
  • Identification of Common Regulators of Genes in Co-Expression Networks Affecting Muscle and Meat Properties
1000 Autor/in
  1. Ponsuksili, Siriluck |
  2. Siengdee, Puntita |
  3. Trakooljul, Nares |
  4. Murani, Eduard |
  5. Schwerin, Manfred |
  6. Du, Yang |
  7. Wimmers, Klaus |
1000 Erscheinungsjahr 2015
1000 LeibnizOpen
1000 Publikationstyp
  1. Artikel |
1000 Online veröffentlicht
  • 2015-04-14
1000 Erschienen in
1000 Quellenangabe
  • 10(4):e0123678
1000 FRL-Sammlung
1000 Copyrightjahr
  • 2015
1000 Lizenz
1000 Verlagsversion
  • |
  • |
1000 Ergänzendes Material
  • |
1000 Publikationsstatus
1000 Begutachtungsstatus
1000 Sprache der Publikation
1000 Abstract/Summary
  • Understanding the genetic contributions behind skeletal muscle composition and metabolism is of great interest in medicine and agriculture. Attempts to dissect these complex traits combine genome-wide genotyping, expression data analyses and network analyses. Weighted gene co-expression network analysis (WGCNA) groups genes into modules based on patterns of co-expression, which can be linked to phenotypes by correlation analysis of trait values and the module eigengenes, i.e. the first principal component of a given module. Network hub genes and regulators of the genes in the modules are likely to play an important role in the emergence of respective traits. In order to detect common regulators of genes in modules showing association with meat quality traits, we identified eQTL for each of these genes, including the highly connected hub genes. Additionally, the module eigengene values were used for association analyses in order to derive a joint eQTL for the respective module. Thereby major sites of orchestrated regulation of genes within trait-associated modules were detected as hotspots of eQTL of many genes of a module and of its eigengene. These sites harbor likely common regulators of genes in the modules. We exemplarily showed the consistent impact of candidate common regulators on the expression of members of respective modules by RNAi knockdown experiments. In fact, Cxcr7 was identified and validated as a regulator of genes in a module, which is involved in the function of defense response in muscle cells. Zfp36l2 was confirmed as a regulator of genes of a module related to cell death or apoptosis pathways. The integration of eQTL in module networks enabled to interpret the differentially-regulated genes from a systems perspective. By integrating genome-wide genomic and transcriptomic data, employing co-expression and eQTL analyses, the study revealed likely regulators that are involved in the fine-tuning and synchronization of genes with trait-associated expression.
1000 Sacherschließung
lokal Gene regulation
lokal Meat
lokal Gene expression
lokal Small interfering RNAs
lokal Apoptosis
lokal Genetic networks
lokal Regulator genes
lokal Muscle cells
1000 Fächerklassifikation (DDC)
1000 Liste der Beteiligten
1000 Label
1000 Förderer
  1. German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) |
1000 Fördernummer
  1. PO753/6-1; WI1754/14-1
1000 Förderprogramm
  1. -
1000 Dateien
1000 Förderung
  1. 1000 joinedFunding-child
    1000 Förderer German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) |
    1000 Förderprogramm -
    1000 Fördernummer PO753/6-1; WI1754/14-1
1000 Objektart article
1000 Beschrieben durch
1000 @id frl:6405342.rdf
1000 Erstellt am 2017-11-08T10:31:03.880+0100
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1000 Bearbeitet von 218
1000 Zuletzt bearbeitet Mon Nov 30 16:31:57 CET 2020
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1000 Vgl. frl:6405342
1000 Oai Id
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