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    A Bayesian model for the identification of differentially expressed genes in Daphnia magna exposed to munition pollutants

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    Author
    Cassese, Alberto; Guindani, Michele; Antczak, Philipp; Falciani, Francesco; Vannucci, Marina
    Date
    2015
    Abstract
    In this article we propose a Bayesian hierarchical model for the identification of differentially expressed genes in Daphnia magna organisms exposed to chemical compounds, specifically munition pollutants in water. The model we propose constitutes one of the very first attempts at a rigorous modeling of the biological effects of water purification. We have data acquired from a purification system that comprises four consecutive purification stages, which we refer to as "ponds," of progressively more contaminated water. We model the expected expression of a gene in a pond as the sum of the mean of the same gene in the previous pond plus a gene-pond specific difference. We incorporate a variable selection mechanism for the identification of the differential expressions, with a prior distribution on the probability of a change that accounts for the available information on the concentration of chemical compounds present in the water. We carry out posterior inference via MCMC stochastic search techniques. In the application, we reduce the complexity of the data by grouping genes according to their functional characteristics, based on the KEGG pathway database. This also increases the biological interpretability of the results. Our model successfully identifies a number of pathways that show differential expression between consecutive purification stages. We also find that changes in the transcriptional response are more strongly associated to the presence of certain compounds, with the remaining contributing to a lesser extent. We discuss the sensitivity of these results to the model parameters that measure the influence of the prior information on the posterior inference.
    Citation
    Cassese, Alberto, Guindani, Michele, Antczak, Philipp, et al.. "A Bayesian model for the identification of differentially expressed genes in Daphnia magna exposed to munition pollutants." Biometrics, 71, no. 3 (2015) Wiley: 803-811. http://dx.doi.org/10.1111/biom.12303.
    Published Version
    http://dx.doi.org/10.1111/biom.12303
    Keyword
    Bayesian inference; Daphnia magna; environmental toxicology; Probit prior; Transcriptomics; More... variable selection Less...
    Type
    Journal article
    Publisher
    Wiley
    Citable link to this page
    https://hdl.handle.net/1911/94231
    Rights
    This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Wiley.
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    • Faculty Publications [4988]
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    Home | FAQ | Contact Us | Privacy Notice | Accessibility Statement
    Managed by the Digital Scholarship Services at Fondren Library, Rice University
    Physical Address: 6100 Main Street, Houston, Texas 77005
    Mailing Address: MS-44, P.O.BOX 1892, Houston, Texas 77251-1892
    Site Map