metaGraphite–a new layer of pathway annotation to get metabolite networks

Bioinformatics (Oxford, England) - Tập 35 Số 7 - Trang 1258-1260 - 2019
Gabriele Sales1, Enrica Calura1, Chiara Romualdi1
1Department of Biology, University of Padova, Padova, Italy

Tóm tắt

AbstractMotivationMetabolomics is an emerging ‘omics’ science involving the characterization of metabolites and metabolism in biological systems. Few bioinformatic tools have been developed for the visualization, exploration and analysis of metabolomic data within the context of metabolic pathways: some of them became rapidly obsolete and are no longer supported, others are based on a single database. A systematic collection of existing annotations has the potential of considerably boosting the investigation and contextualization of metabolomic measurements.ResultsWe have released a major update of our Bioconductor package graphite which explicitly tracks small molecules within pathway topologies and their interactions with proteins. The package gathers the information stored in eight major databases, oriented both at genes and at metabolites, across 14 different species. Depending on user preferences, all pathways can be retrieved as gene-only, gene metabolite or metabolite-only networks.Availability and implementationThe new graphite version (1.24) is available on Bioconductor.Supplementary informationSupplementary data are available at Bioinformatics online.

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Bioinformatics (Oxford, England)

Tập 35 Số 7

1258-1260

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