title: Identification of gene co-expression clusters in liver tissues from multiple porcine populations with high and low backfat androstenone phenotype.
abstract: BACKGROUND
  Boar taint is principally caused by accumulation of androstenone and skatole in adipose tissues. Studies have shown high heritability estimates for androstenone whereas skatole production is mainly dependent on nutritional factors. Androstenone is a lipophilic steroid mainly metabolized in liver. Majority of the studies on hepatic androstenone metabolism focus only on a single breed and very few studies account for population similarities/differences in gene expression patterns. In this work, we concentrated on population similarities in gene expression to identify the common genes involved in hepatic androstenone metabolism of multiple pig populations. Based on androstenone measurements, publicly available gene expression datasets from three porcine populations were compiled into either low or high androstenone dataset. Gene expression correlation coefficients from these datasets were converted to rank ratios and joint probabilities of these rank ratios were used to generate dataset specific co-expression clusters. Finally, these networks were clustered using a graph clustering technique.
  
  
  RESULTS
  Cluster analysis identified a number of statistically significant co-expression clusters in the dataset. Further enrichment analysis of these clusters showed that one of the clusters from low androstenone dataset was highly enriched for xenobiotic, drug, cholesterol and lipid metabolism and cytochrome P450 associated metabolism of drugs and xenobiotics. Literature references revealed that a number of genes in this cluster were involved in phase I and phase II metabolism. Physical and functional similarity assessment showed that the members of this cluster were dispersed across multiple clusters in high androstenone dataset, possibly indicating a weak co-expression of these genes in high androstenone dataset.
  
  
  CONCLUSIONS
  Based on these results we hypothesize that majority of the genes in this cluster forms a signature co-expression cluster in low androstenone dataset in our experiment and that majority of the members of this cluster might be responsible for hepatic androstenone metabolism across all the three populations used in our study. We propose these results as a background work towards understanding breed similarities in hepatic androstenone metabolism. Additional large scale experiments using data from multiple porcine breeds are necessary to validate these findings.
authors.affiliation: Institute of Animal Science, University of Bonn, Endenicher Alle, Bonn, 53115, Germany. ssud@itw.uni-bonn.de.|Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, 53754, Germany. ssud@itw.uni-bonn.de.
authors.forename: Sudeep
authors.initials: S
authors.lastname: Sahadevan
authors.affiliation: Institute of Animal Science, University of Bonn, Endenicher Alle, Bonn, 53115, Germany. ernst.tholen@itw.uni-bonn.de.
authors.forename: Ernst
authors.initials: E
authors.lastname: Tholen
authors.affiliation: Institute of Animal Science, University of Bonn, Endenicher Alle, Bonn, 53115, Germany. cgro@itw.uni-bonn.de.
authors.forename: Christine
authors.initials: C
authors.lastname: Große-Brinkhaus
authors.affiliation: Institute of Animal Science, University of Bonn, Endenicher Alle, Bonn, 53115, Germany. ksch@itw.uni-bonn.de.
authors.forename: Karl
authors.initials: K
authors.lastname: Schellander
authors.affiliation: Institute of Animal Science, University of Bonn, Endenicher Alle, Bonn, 53115, Germany. dtes@itw.uni-bonn.de.
authors.forename: Dawit
authors.initials: D
authors.lastname: Tesfaye
authors.affiliation: Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, 53754, Germany. martin.hofmann-apitius@scai.fraunhofer.de.
authors.forename: Martin
authors.initials: M
authors.lastname: Hofmann-Apitius
authors.affiliation: Department of Animal Science, Faculty of Agriculture, Erciyes University, Kayseri, Turkey. ucin@itw.uni-bonn.de.
authors.forename: Mehmet Ulas
authors.initials: MU
authors.lastname: Cinar
authors.affiliation: Department of Animal Production and Technology, Bogor Agricultural University, Bogor, Indonesia. agun@itw.uni-bonn.de.
authors.forename: Asep
authors.initials: A
authors.lastname: Gunawan
authors.affiliation: Institute of Animal Science, University of Bonn, Endenicher Alle, Bonn, 53115, Germany. mhoe@itw.uni-bonn.de.
authors.forename: Michael
authors.initials: M
authors.lastname: Hölker
authors.affiliation: Institute of Animal Science, University of Bonn, Endenicher Alle, Bonn, 53115, Germany. christiane.neuhoff@itw.uni-bonn.de.
authors.forename: Christiane
authors.initials: C
authors.lastname: Neuhoff
mesh_terms: D000273:Adipose Tissue / Q000378:metabolism*; D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology; D066264:Datasets as Topic; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D008099:Liver / Q000378:metabolism*; D013552:Swine