title: Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.
abstract: BACKGROUND
  The application of high-throughput genomic tools in nutrition research is a widespread practice. However, it is becoming increasingly clear that the outcome of individual expression studies is insufficient for the comprehensive understanding of such a complex field. Currently, the availability of the large amounts of expression data in public repositories has opened up new challenges on microarray data analyses. We have focused on PPARalpha, a ligand-activated transcription factor functioning as fatty acid sensor controlling the gene expression regulation of a large set of genes in various metabolic organs such as liver, small intestine or heart. The function of PPARalpha is strictly connected to the function of its target genes and, although many of these have already been identified, major elements of its physiological function remain to be uncovered. To further investigate the function of PPARalpha, we have applied a cross-species meta-analysis approach to integrate sixteen microarray datasets studying high fat diet and PPARalpha signal perturbations in different organisms.
  
  
  RESULTS
  We identified 164 genes (MDEGs) that were differentially expressed in a constant way in response to a high fat diet or to perturbations in PPARs signalling. In particular, we found five genes in yeast which were highly conserved and homologous of PPARalpha targets in mammals, potential candidates to be used as models for the equivalent mammalian genes. Moreover, a screening of the MDEGs for all known transcription factor binding sites and the comparison with a human genome-wide screening of Peroxisome Proliferating Response Elements (PPRE), enabled us to identify, 20 new potential candidate genes that show, both binding site, both change in expression in the condition studied. Lastly, we found a non random localization of the differentially expressed genes in the genome.
  
  
  CONCLUSIONS
  The results presented are potentially of great interest to resume the currently available expression data, exploiting the power of in silico analysis filtered by evolutionary conservation. The analysis enabled us to indicate potential gene candidates that could fill in the gaps with regards to the signalling of PPARalpha and, moreover, the non-random localization of the differentially expressed genes in the genome, suggest that epigenetic mechanisms are of importance in the regulation of the transcription operated by PPARalpha.
authors.affiliation: Department of Pharmacology, University of Firenze, Firenze, Italy. duccio.cavalieri@unifi.it
authors.forename: Duccio
authors.initials: D
authors.lastname: Cavalieri
authors.forename: Enrica
authors.initials: E
authors.lastname: Calura
authors.forename: Chiara
authors.initials: C
authors.lastname: Romualdi
authors.forename: Emmanuela
authors.initials: E
authors.lastname: Marchi
authors.forename: Marijana
authors.initials: M
authors.lastname: Radonjic
authors.forename: Ben
authors.initials: B
authors.lastname: Van Ommen
authors.forename: Michael
authors.initials: M
authors.lastname: Müller
mesh_terms: D000818:Animals; D001665:Binding Sites; D016000:Cluster Analysis; D055028:Comparative Genomic Hybridization / Q000379:methods*; D019295:Computational Biology; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D051379:Mice; D054647:Nutrigenomics; D020411:Oligonucleotide Array Sequence Analysis; D047493:PPAR alpha / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics
chemical_list: D047493:PPAR alpha; D014157:Transcription Factors