MetaboSignal: a Network-based Approach for Topological Analysis of Metabotype Regulation Via Metabolic and Signaling Pathways

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2016 Dec 25

PMID 28011775

Citations 12

Authors

Andrea Rodriguez-Martinez

Rafael Ayala

Joram M Posma

Ana L Neves

Dominique Gauguier

Jeremy K Nicholson

Marc-Emmanuel Dumas

Affiliations

Soon will be listed here.

Abstract

Summary: MetaboSignal is an R package that allows merging metabolic and signaling pathways reported in the Kyoto Encyclopaedia of Genes and Genomes (KEGG). It is a network-based approach designed to navigate through topological relationships between genes (signaling- or metabolic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape of metabolic phenotypes.

Availability And Implementation: MetaboSignal is available from Bioconductor: https://bioconductor.org/packages/MetaboSignal/.

Contact: m.dumas@imperial.ac.uk .

Supplementary Information: Supplementary data are available at Bioinformatics online.

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References

Davidovic L, Navratil V, Bonaccorso C, Catania M, Bardoni B, Dumas M . A metabolomic and systems biology perspective on the brain of the fragile X syndrome mouse model. Genome Res. 2011; 21(12):2190-202. PMC: 3227107. DOI: 10.1101/gr.116764.110. View

Zhang J, Wiemann S . KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor. Bioinformatics. 2009; 25(11):1470-1. PMC: 2682514. DOI: 10.1093/bioinformatics/btp167. View

Kanehisa M, Goto S . KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 1999; 28(1):27-30. PMC: 102409. DOI: 10.1093/nar/28.1.27. View

Nicholson J, Connelly J, Lindon J, Holmes E . Metabonomics: a platform for studying drug toxicity and gene function. Nat Rev Drug Discov. 2002; 1(2):153-61. DOI: 10.1038/nrd728. View

Wada T, Sasaoka T, Funaki M, Hori H, Murakami S, Ishiki M . Overexpression of SH2-containing inositol phosphatase 2 results in negative regulation of insulin-induced metabolic actions in 3T3-L1 adipocytes via its 5'-phosphatase catalytic activity. Mol Cell Biol. 2001; 21(5):1633-46. PMC: 86709. DOI: 10.1128/MCB.21.5.1633-1646.2001. View

Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498-504. PMC: 403769. DOI: 10.1101/gr.1239303. View

Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M . Towards a knowledge-based Human Protein Atlas. Nat Biotechnol. 2010; 28(12):1248-50. DOI: 10.1038/nbt1210-1248. View

Posma J, Robinette S, Holmes E, Nicholson J . MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG. Bioinformatics. 2013; 30(6):893-5. PMC: 3957072. DOI: 10.1093/bioinformatics/btt612. View

Dumas M, Domange C, Calderari S, Martinez A, Ayala R, Wilder S . Topological analysis of metabolic networks integrating co-segregating transcriptomes and metabolomes in type 2 diabetic rat congenic series. Genome Med. 2016; 8(1):101. PMC: 5045612. DOI: 10.1186/s13073-016-0352-6. View

10.

Dumas M . Metabolome 2.0: quantitative genetics and network biology of metabolic phenotypes. Mol Biosyst. 2012; 8(10):2494-502. DOI: 10.1039/c2mb25167a. View

11.

Cottret L, Wildridge D, Vinson F, Barrett M, Charles H, Sagot M . MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Res. 2010; 38(Web Server issue):W132-7. PMC: 2896158. DOI: 10.1093/nar/gkq312. View

12.

Rodgers J, Vogel R, Puigserver P . Clk2 and B56β mediate insulin-regulated assembly of the PP2A phosphatase holoenzyme complex on Akt. Mol Cell. 2011; 41(4):471-9. PMC: 3060660. DOI: 10.1016/j.molcel.2011.02.007. View