Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics

Pathway analysis, originally developed for gene expression data, has been adapted for metabolomics. However, owing to the unique characteristics and constraints of metabolites compared with

genes, pathway analysis in metabolomics often yields misleading or nonsensical results. Access through your institution Buy or subscribe This is a preview of subscription content, access via

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institutional subscriptions * Read our FAQs * Contact customer support REFERENCES * Khatri, P., Sirota, M. & Butte, A. J. _PLoS Comput. Biol._ 8, e1002375 (2012). Article  CAS  PubMed 

PubMed Central  Google Scholar  * García-Campos, M. A., Espinal-Enríquez, J. & Hernández-Lemus, E. _Front. Physiol._ 6, 383 (2015). Article  PubMed  PubMed Central  Google Scholar  *

Johnson, C. H., Ivanisevic, J. & Siuzdak, G. _Nat. Rev. Mol. Cell Biol._ 17, 451–459 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  * Huan, T. et al. _Nat. Methods_ 14,

461–462 (2017). Article  CAS  PubMed  PubMed Central  Google Scholar  * Pang, Z. et al. _Nat. Protoc._ 17, 1735–1761 (2022). Article  CAS  PubMed  Google Scholar  * Wollman, A. J. et al.

_eLife_ 6, e27451 (2017). Article  PubMed  PubMed Central  Google Scholar  * Subramanian, A. et al. _Proc. Natl Acad. Sci. USA_ 102, 15545–15550 (2005). Article  CAS  PubMed  PubMed Central

  Google Scholar  * Tanner, L. B. et al. _Cell Syst._ 7, 49–62.e8 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  * Baker, S. A. & Rutter, J. _Nat. Rev. Mol. Cell Biol._

24, 355–374 (2023). Article  CAS  PubMed  Google Scholar  * Han, J. et al. _Metabolomics_ 4, 128–140 (2008). Article  CAS  PubMed  PubMed Central  Google Scholar  * Sindelar, M. & Patti,

G. J. _J. Am. Chem. Soc._ 142, 9097–9105 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Ye, D., Guan, K.-L. & Xiong, Y. _Trends Cancer_ 4, 151–165 (2018). Article  CAS

  PubMed  PubMed Central  Google Scholar  * Schymanski, E. L. et al. _Environ. Sci. Technol._ 48, 2097–2098 (2014). Article  CAS  PubMed  Google Scholar  * Yang, X. et al. _Nat. Genet._ 41,

415–423 (2009). Article  CAS  PubMed  PubMed Central  Google Scholar  * Zamboni, N., Fendt, S.-M., Rühl, M. & Sauer, U. _Nat. Protoc._ 4, 878–892 (2009). Article  CAS  PubMed  Google

Scholar  Download references ACKNOWLEDGEMENTS The project was supported by grants from Canada Research Chair Program (AWD-029086), National Cancer Institute – Cancer Center Support Grant

(P30CA072720-6852) and Fundação Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (88887.937782/2024-00). We also thank A. Hui for proofreading this manuscript. AUTHOR INFORMATION

AUTHORS AND AFFILIATIONS * Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil Kil Sun Lee * Department of Medicine, Robert Wood

Johnson Medical School, Rutgers University, New Brunswick, NJ, USA Xiaoyang Su * Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver Campus, Vancouver,

British Columbia, Canada Tao Huan Authors * Kil Sun Lee View author publications You can also search for this author inPubMed Google Scholar * Xiaoyang Su View author publications You can

also search for this author inPubMed Google Scholar * Tao Huan View author publications You can also search for this author inPubMed Google Scholar CORRESPONDING AUTHORS Correspondence to

Xiaoyang Su or Tao Huan. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing interests. PEER REVIEW PEER REVIEW INFORMATION _Nature Metabolism_ thanks Martin Giera and

the other, anonymous, reviewer(s) for their contribution to the peer review of this work. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Lee, K.S., Su,

X. & Huan, T. Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics. _Nat Metab_ 7, 858–861 (2025). https://doi.org/10.1038/s42255-025-01283-0 Download

citation * Published: 10 April 2025 * Issue Date: May 2025 * DOI: https://doi.org/10.1038/s42255-025-01283-0 SHARE THIS ARTICLE Anyone you share the following link with will be able to read

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