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

Nature

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


Play all audios:

Loading...

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


your institution ACCESS OPTIONS Access through your institution Access Nature and 54 other Nature Portfolio journals Get Nature+, our best-value online-access subscription $29.99 / 30 days


cancel any time Learn more Subscribe to this journal Receive 12 digital issues and online access to articles $119.00 per year only $9.92 per issue Learn more Buy this article * Purchase on


SpringerLink * Instant access to full article PDF Buy now Prices may be subject to local taxes which are calculated during checkout ADDITIONAL ACCESS OPTIONS: * Log in * Learn about


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


this content: Get shareable link Sorry, a shareable link is not currently available for this article. Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative


Trending News

Three Seasons In, And Just Like That Is Finally Its Own Gloriously Preposterous Thing

Carrie Bradshaw never stops starting over. After the original Sex and the City series ended with Sarah Jessica Parker’s ...

Hamas leader mohammed sinwar killed, netanyahu says

Hamas’s de facto leader in Gaza, Mohammed Sinwar, was killed during a recent airstrike, Israeli Prime Minister Netanyahu...

Who are todd and julie chrisley, whom trump is pardoning?

President Donald Trump announced Tuesday that he would be pardoning reality TV stars Todd and Julie Chrisley, a couple b...

Why the u. S. Is pausing student visa interviews at embassies

Prospective international students to the U.S. were dealt another blow when U.S. embassies were ordered not to schedule ...

Should you take a vitamin d supplement?

Vitamin D does a lot for your body, supporting strong bones, muscle movement, your immune system, and more. Taking a vit...

Latests News

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 th...

Google maps street view: woman caught in awkward position

Google Maps Street View has caught some of the funniest situations across the globe by accident. While the cars are mean...

Best practices and tools for reporting reproducible fluorescence microscopy methods

ABSTRACT Although fluorescence microscopy is ubiquitous in biomedical research, microscopy methods reporting is inconsis...

Foundations of mathematical genetics (2nd edn).

Foundations of Mathematical Genetics (2nd edn). Anthony W. F. Edwards. Cambridge University Press, Cambridge. 2000. Pp. ...

Generating destination brand awareness and image through the firm's social media

Pragmatically, the findings of this study urge policymakers of tourism companies, managers and destination marketers to ...

Top