Abstract
The field of metabolomics, one of the omics technologies that have recently revolutionized biological research, provides multiple challenges for data analysis, that have been addressed by several computational tools. However, none addresses the multiplicity of existing techniques and data analysis tasks. Here, we propose a novel R package that provides a set of functions for metabolomics data analysis, including data loading in different formats, pre-processing, univariate and multivariate data analysis, machine learning and feature selection. The package supports the analysis of data from the main experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment, promoting the rapid development and sharing of data analysis pipelines.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Banskota, A.H., Tezuka, Y., Kadota, S.H.: Recent progress in pharmacological research of propolis. Phytother. Res. 15, 561–571 (2001)
Beleites, C.: hyperSpec introduction. URL http://cran.r-project.org/web/packages/hyperSpec/vignettes/introduction.pdf. CENMAT and DI3, University of Trieste Spectroscopy - Imaging, IPHT Jena e.V (2014)
Burdock, G.A.: Review of the biological properties and toxicity of bee propolis (propolis). Food Chem. Toxicol. 36, 347–363 (1998)
Eisner, R., Stretch, C., Eastman, T., Xia, J., Hau, D., Damaraju, S., Greiner, R., Wishart, D.S., Baracos, V.E.: Learning to predict cancer-associated skeletal muscle wasting from 1h-nmr profiles of urinary metabolites. Metabolomics 7, 25–34 (2010)
Evans, W.J., Morleya, J.E., Argilésa, J., Balesa, C., Baracosa, V., Guttridgea, D., Jatoia, A., Kalantar-Zadeha, K., Lochsa, H., Mantovania, G., Marksa, D., Mitcha, W.E., Muscaritolia, M., Najanda, A., Ponikowskia, P., Fanellia, F.R., Schambelana, M., Scholsa, A., Schustera, M., Thomas, D., Wolfea, R., Anker, S.D.: Cachexia: a new definition. Clin. Nutr. 27, 793–799 (2008)
Gekker, G., Hu, S., Spivak, M., Lokensgard, J.R., Peterson, P.K.: Anti-hiv-1 activity of propolis in cd4+ lymphocyte and microglial cell cultures. J. Ethnopharmacol. 102, 158–163 (2005)
Hanson, B.A.: Chemospec: an r package for chemometric analysis of spectroscopic data and chromatograms (2013)
Kumazawa, S., Ueda, R., Hamasaka, T., Fukumoto, S., Fujimoto, T., Nakayama, T.: Antioxidant prenylated flavonoids from propolis collected in Okinawa, Japan. J. Agric. Food Chem. 55, 7722–7725 (2007)
Mozzi, F., Ortiz, M.E., Bleckwedel, J., Vuyst, L.D., Pescuma, M.: Metabolomics as a tool for the comprehensive understanding of fermented and functional foods with lactic acid bacteria. Food Res. Int. (2012)
Nielsen, J., Jewett, M.C.: Metabolomics: A Powerful Tool in Systems Biology. Springer, Berlin (2007)
Sforcin, J.M.: Propolis and the immune system: a review. J. Ethnopharmacol. 113, 1–14 (2007)
Tan-No, K., Nakajima, K.T., Shoii, T., Nakagawasai, O., Niijima, F., Ishikawa, M., Endo, Y., Sato, T., Satoh, S., Tadano, K.: Anti-inflammatory effect of própolis through nitric oxide production on carrageenin-induced mouse paw edema. Biol. Pharm. Bull 29, 96–99 (2006)
Uarrota, V.G., Moresco, R., Coelho, B., da Costa, E.: In: Nunes, L.A., Martins Peruch, E., de Oliveira Neubert, M., Rocha, M.M. (eds.) Metabolomics combined with chemometric tools (pca, hca, pls-da and svm) for screening cassava (manihot esculenta crantz) roots during postharvest physiological deterioration. Food Chem. 161, 67–78 (2014)
Varmuza, K., Filzmoser, P.: Introduction to multivariate statistical analysis in chemometrics. (2008, CRC Press)
Villas-Boas, S., Roessner, U., Hansen, M.A.E., Smedsgaard, J., Nielsen, J.: Metabolome analysis: an introduction. Wiley, Hoboken (2007)
Xia, J., Mandal, R., Sinelnikov, I.V., Broadhurst, D., Wishart, D.S.: Metaboanalyst 2.0-a comprehensive server for metabolomic data analysis. Nucleic Acids Res. 40, 127–33 (2012)
Smith, C.A., Want, E.J., O’Maille, G., Abagyan, R., Siuzdak, G.: XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification. Anal. Chem. 78, 779–787 (2006)
Acknowledgments
The work is partially funded by Project 23060, PEM - Technological Support Platform for Metabolic Engineering, co- funded by FEDER through Portuguese QREN under the scope of the Technological Research and Development Incentive system, North Operational and by Project PropMine, funded by the agreement between Portuguese FCT and Brazilian CNPq.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Costa, C., Maraschin, M., Rocha, M. (2015). An Integrated Computational Platform for Metabolomics Data Analysis. In: Overbeek, R., Rocha, M., Fdez-Riverola, F., De Paz, J. (eds) 9th International Conference on Practical Applications of Computational Biology and Bioinformatics. Advances in Intelligent Systems and Computing, vol 375. Springer, Cham. https://doi.org/10.1007/978-3-319-19776-0_5
Download citation
DOI: https://doi.org/10.1007/978-3-319-19776-0_5
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-19775-3
Online ISBN: 978-3-319-19776-0
eBook Packages: EngineeringEngineering (R0)