Intertwining threshold settings, biological data and database knowledge to optimize the selection of differentially expressed genes from microarray

Chuchana Paul, Holzmuller Philippe, Vezilier Frédéric, Berthier David, Chantal Isabelle, Severac Dany, Lemesre Jean-Loup, Cuny Gérard, Nirdé Philippe, Bucheton Bruno. 2010. Intertwining threshold settings, biological data and database knowledge to optimize the selection of differentially expressed genes from microarray. PloS One, 5 (10):e13518, 12 p.

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Quartile : Q1, Sujet : BIOLOGY

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie; Staps

Abstract : Background: Many tools used to analyze microarrays in different conditions have been described. However, the integration of deregulated genes within coherent metabolic pathways is lacking. Currently no objective selection criterion based on biological functions exists to determine a threshold demonstrating that a gene is indeed differentially expressed. Methodology/Principal Findings: To improve transcriptomic analysis of microarrays, we propose a new statistical approach that takes into account biological parameters. We present an iterative method to optimise the selection of differentially expressed genes in two experimental conditions. The stringency level of gene selection was associated simultaneously with the p-value of expression variation and the occurrence rate parameter associated with the percentage of donors whose transcriptomic profile is similar. Our method intertwines stringency level settings, biological data and a knowledge database to highlight molecular interactions using networks and pathways. Analysis performed during iterations helped us to select the optimal threshold required for the most pertinent selection of differentially expressed genes. Conclusions/Significance: We have applied this approach to the well documented mechanism of human macrophage response to lipopolysaccharide stimulation. We thus verified that our method was able to determine with the highest degree of accuracy the best threshold for selecting genes that are truly differentially expressed. (Résumé d'auteur)

Mots-clés Agrovoc : Gène, Expression des gènes, Banque de données, Sélection, ADN, Sélection individuelle, génétique animale, Modèle mathématique, Logiciel

Mots-clés complémentaires : Puce à ADN, Expression du gène

Classification Agris : U10 - Computer science, mathematics and statistics
C30 - Documentation and information
U30 - Research methods
L10 - Animal genetics and breeding
000 - Other themes

Champ stratégique Cirad : Hors axes (2005-2013)

Auteurs et affiliations

  • Chuchana Paul, IRD (FRA)
  • Holzmuller Philippe, CIRAD-BIOS-UMR TRYPANOSOMES (FRA) ORCID: 0000-0002-8919-9081
  • Berthier David, CIRAD-BIOS-UMR TRYPANOSOMES (FRA) ORCID: 0000-0002-3283-6588
  • Chantal Isabelle, CIRAD-BIOS-UMR TRYPANOSOMES (FRA) ORCID: 0000-0002-3429-484X
  • Severac Dany, Montpellier Génopole Microarray Facility (FRA)
  • Lemesre Jean-Loup, IRD (FRA)
  • Cuny Gérard, IRD (FRA)
  • Nirdé Philippe, INSERM (FRA)

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