@article{fdi:010052860,
  title = {{I}ntertwining threshold settings, biological data and database knowledge to optimize the selection of differentially expressed genes from microarray},
  author = {{C}huchana, {P}aul and {H}olzmuller, {P}. and {V}{\'e}zilier, {F}. and {B}erthier, {D}. and {C}hantal, {I}. and {S}{\'e}verac, {D}. and {L}emesre, {J}ean-{L}oup and {C}uny, {G}{\'e}rard and {N}ird{\'e}, {P}. and {B}ucheton, {B}runo},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {M}any tools used to analyze microarrays in different conditions have been described. {H}owever, the integration of deregulated genes within coherent metabolic pathways is lacking. {C}urrently no objective selection criterion based on biological functions exists to determine a threshold demonstrating that a gene is indeed differentially expressed. {M}ethodology/{P}rincipal {F}indings: {T}o improve transcriptomic analysis of microarrays, we propose a new statistical approach that takes into account biological parameters. {W}e present an iterative method to optimise the selection of differentially expressed genes in two experimental conditions. {T}he 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. {O}ur method intertwines stringency level settings, biological data and a knowledge database to highlight molecular interactions using networks and pathways. {A}nalysis performed during iterations helped us to select the optimal threshold required for the most pertinent selection of differentially expressed genes. {C}onclusions/{S}ignificance: {W}e have applied this approach to the well documented mechanism of human macrophage response to lipopolysaccharide stimulation. {W}e 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.},
  keywords = {},
  booktitle = {},
  journal = {{P}los {O}ne},
  volume = {5},
  numero = {10},
  pages = {e13518},
  ISSN = {1932-6203},
  year = {2010},
  DOI = {10.1371/journal.pone.0013518},
  URL = {https://www.documentation.ird.fr/hor/fdi:010052860},
}