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A mathematical framework for spectroscopy data analysis to characterize chemical-induced alterations in the SHE assay

Trevisan, Julio and Angelov, Plamen P. and Carmichael, Paul L. and Scott, Andrew D. and Martin, Francis L. (2010) A mathematical framework for spectroscopy data analysis to characterize chemical-induced alterations in the SHE assay. Mutagenesis, 25 (6). p. 658. ISSN 0267-8357

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Abstract

Acquisition of IR spectra often generates complex datasets that are not readily interpretable for the purposes of deriving biomarkers. From a computational perspective, this raises the question of what multi-step processing is required and, whether there is a well-defined sequence of steps that can be applied to objectively shed insight into a biological question. To generate a dataset to investigate this, we set up an in vitro transformation assay (pH 6.7) using Syrian hamster embryo (SHE) cells (1). SHE cells were interrogated by ATR-FTIR spectroscopy. Derived mid-IR spectra (nspectra @14,000) were inputted into a computational framework designed for outlier removal, multivariate analysis and validation of the robustness of analysis, and biomarker identification. Biomarker identification methods were independently applied and compared to identify common discriminating chemical entities. Stable biomarkers of chemical-induced alterations or transformation were identified and confirmed. The analysis framework was implemented in the form of a user-friendly graphical user interface using a programming toolkit designed for research on computational methods. The database platform developed to store our dataset is scalable and can facilitate a data-sharing inter-laboratory process towards end-user applications for IR spectroscopy.

Item Type: Article
Journal or Publication Title: Mutagenesis
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Departments: Faculty of Science and Technology > School of Computing & Communications
Faculty of Science and Technology > Lancaster Environment Centre
ID Code: 58024
Deposited By: ep_importer_pure
Deposited On: 02 Oct 2012 16:14
Refereed?: Yes
Published?: Published
Last Modified: 03 Jun 2014 17:16
Identification Number:
URI: http://eprints.lancs.ac.uk/id/eprint/58024

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