Dataset Information

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.

Conclusion

This study has demonstrated that our approach is promising for bioavailability measurement, which warrants further studies of mixed contamination scenarios in field settings.

SUBMITTER: Gong P

PROVIDER: S-EPMC4784335 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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Publications

Predicting chemical bioavailability using microarray gene expression data and regression modeling: A tale of three explosive compounds.

Gong Ping P Nan Xiaofei X Barker Natalie D ND Boyd Robert E RE Chen Yixin Y Wilkins Dawn E DE Johnson David R DR Suedel Burton C BC Perkins Edward J EJ

BMC genomics 20160308

<h4>Background</h4>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 ...[more]

PMID: 26956490

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Dataset Information

Predicting chemical bioavailability using microarray gene expression data and regression modeling: A tale of three explosive compounds.

Background

Results

Conclusion

Publications

Predicting chemical bioavailability using microarray gene expression data and regression modeling: A tale of three explosive compounds.

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