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

MOTIVATION Metabolomics 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. RESULTS We 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 IMPLEMENTATION The new graphite version (1.24) is available on Bioconductor. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

[1]  P. Khatri,et al.  A systems biology approach for pathway level analysis. , 2007, Genome research.

[2]  Pooja Mittal,et al.  A novel signaling pathway impact analysis , 2009, Bioinform..

[3]  Yumei Song,et al.  A Novel Signaling Pathway , 2009, The Journal of Biological Chemistry.

[4]  Monica Chiogna,et al.  Gene set analysis exploiting the topology of a pathway , 2010, BMC Systems Biology.

[5]  Michael P. Barrett,et al.  MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks , 2010, Nucleic Acids Res..

[6]  Gabriele Sales,et al.  graphite - a Bioconductor package to convert pathway topology to gene network , 2012, BMC Bioinformatics.

[7]  Cristina Mitrea,et al.  Methods and approaches in the topology-based analysis of biological pathways , 2013, Front. Physiol..

[8]  Monica Chiogna,et al.  Along signal paths: an empirical gene set approach exploiting pathway topology , 2012, Nucleic acids research.

[9]  Sarah J. Kurley,et al.  MYC-driven accumulation of 2-hydroxyglutarate is associated with breast cancer prognosis. , 2014, The Journal of clinical investigation.

[10]  Joram M. Posma,et al.  MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG , 2013, Bioinform..

[11]  D. Wishart.  Emerging applications of metabolomics in drug discovery and precision medicine , 2016, Nature Reviews Drug Discovery.

[12]  Joram M. Posma,et al.  MetaboSignal: a network-based approach for topological analysis of metabotype regulation via metabolic and signaling pathways , 2016, Bioinform..