title: Predicting chemical bioavailability using microarray gene expression data and regression modeling: A tale of three explosive compounds.
abstract: BACKGROUND
  Chemical bioavailability is an important dose metric in environmental risk assessment. Although many approaches have been used to evaluate bioavailability, not a single approach is free from limitations. Previously, we developed a new genomics-based approach that integrated microarray technology and regression modeling for predicting bioavailability (tissue residue) of explosives compounds in exposed earthworms. In the present study, we further compared 18 different regression models and performed variable selection simultaneously with parameter estimation.
  
  
  RESULTS
  This refined approach was applied to both previously collected and newly acquired earthworm microarray gene expression datasets for three explosive compounds. Our results demonstrate that a prediction accuracy of R(2) = 0.71-0.82 was achievable at a relatively low model complexity with as few as 3-10 predictor genes per model. These results are much more encouraging than our previous ones.
  
  
  CONCLUSIONS
  This study has demonstrated that our approach is promising for bioavailability measurement, which warrants further studies of mixed contamination scenarios in field settings.
authors.affiliation: Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA. ping.gong@usace.army.mil.
authors.forename: Ping
authors.initials: P
authors.lastname: Gong
authors.affiliation: Department of Computer and Information Science, University of Mississippi, Oxford, Mississippi, 38677, USA. iexfnan@zzu.edu.cn.|Present Address: School of Information Engineering, Zhengzhou University, Zhengzhou, Henan, 450001, China. iexfnan@zzu.edu.cn.
authors.forename: Xiaofei
authors.initials: X
authors.lastname: Nan
authors.affiliation: Bennett Aerospace Inc., Cary, North Carolina, 27518, USA. Natalie.D.Barker@usace.army.mil.
authors.forename: Natalie D
authors.initials: ND
authors.lastname: Barker
authors.affiliation: Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA. Robert.E.Boyd@usace.army.mil.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Boyd
authors.affiliation: Department of Computer and Information Science, University of Mississippi, Oxford, Mississippi, 38677, USA. ychen@cs.olemiss.edu.
authors.forename: Yixin
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Department of Computer and Information Science, University of Mississippi, Oxford, Mississippi, 38677, USA. dwilkins@cs.olemiss.edu.
authors.forename: Dawn E
authors.initials: DE
authors.lastname: Wilkins
authors.affiliation: GHD, Dallas, Texas, 75234, USA. david.r.johnson@ghd.com.
authors.forename: David R
authors.initials: DR
authors.lastname: Johnson
authors.affiliation: Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA. Burton.Suedel@usace.army.mil.
authors.forename: Burton C
authors.initials: BC
authors.lastname: Suedel
authors.affiliation: Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA. Edward.J.Perkins@usace.army.mil.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Perkins
mesh_terms: D000818:Animals; D001392:Azocines / Q000493:pharmacokinetics; D001682:Biological Availability; D053834:Explosive Agents / Q000493:pharmacokinetics*; D020869:Gene Expression Profiling / Q000379:methods*; D009835:Oligochaeta / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D012044:Regression Analysis; D012989:Soil Pollutants / Q000493:pharmacokinetics*; D014227:Triazines / Q000493:pharmacokinetics; D014303:Trinitrotoluene / Q000493:pharmacokinetics
chemical_list: D001392:Azocines; D053834:Explosive Agents; D012989:Soil Pollutants; D014227:Triazines; D014303:Trinitrotoluene; C007950:octogen; C009160:cyclonite