title: Molecular toxicity identification evaluation (mTIE) approach predicts chemical exposure in Daphnia magna.
abstract: Daphnia magna is a bioindicator organism accepted by several international water quality regulatory agencies. Current approaches for assessment of water quality rely on acute and chronic toxicity that provide no insight into the cause of toxicity. Recently, molecular approaches, such as genome wide gene expression responses, are enabling an alternative mechanism based approach to toxicity assessment. While these genomic methods are providing important mechanistic insight into toxicity, statistically robust prediction systems that allow the identification of chemical contaminants from the molecular response to exposure are needed. Here we apply advanced machine learning approaches to develop predictive models of contaminant exposure using a D. magna gene expression data set for 36 chemical exposures. We demonstrate here that we can discriminate between chemicals belonging to different chemical classes including endocrine disruptors and inorganic and organic chemicals based on gene expression. We also show that predictive models based on indices of whole pathway transcriptional activity can achieve comparable results while facilitating biological interpretability.
authors.affiliation: Centre for Computational Biology and Modelling, Institute for Integrative Biology, University of Liverpool , L69 7ZB Liverpool, U.K..
authors.forename: Philipp
authors.initials: P
authors.lastname: Antczak
authors.forename: Hun Je
authors.initials: HJ
authors.lastname: Jo
authors.forename: Seonock
authors.initials: S
authors.lastname: Woo
authors.forename: Leona
authors.initials: L
authors.lastname: Scanlan
authors.forename: Helen
authors.initials: H
authors.lastname: Poynton
authors.forename: Alex
authors.initials: A
authors.lastname: Loguinov
authors.forename: Sarah
authors.initials: S
authors.lastname: Chan
authors.forename: Francesco
authors.initials: F
authors.lastname: Falciani
authors.forename: Chris
authors.initials: C
authors.lastname: Vulpe
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D003621:Daphnia / Q000187:drug effects* / Q000235:genetics; D004784:Environmental Monitoring; D004785:Environmental Pollutants / Q000633:toxicity*; D008957:Models, Genetic; D018675:Toxicity Tests / Q000379:methods*; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D004785:Environmental Pollutants