Analysing the structure of pathways and its influence on the interpretation of biomedical datasets
Open accessPreprint — published as 10.1021/acs.jproteome.8b00464 · Paper page
Abstract
Summary: Biochemical pathways are commonly used as a reference to conduct functional analysis on biomedical omics datasets, where experimental results are mapped to knowledgebases comprising known molecular interactions collected from the literature. Due to their central role, the content of the functional knowledgebases directly influences the outcome of pathway analyses. In this study, we investigate the structure of the current pathway knowledge, as exemplified by Reactome, discuss the consequences for biological interpretation, and outline possible improvements in the use of pathway knowledgebases. By providing a view of the underlying network structure, we aim to help pathway analysis users manage their expectations and better identify possible artefacts in the results.
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Cites
Proteoform: a single term describing protein complexity
The Consortium for Top Down Proteomics, Smith, L. M., & Kelleher, N. L. (2013) · Nature Methods · doi:10.1038/nmeth.2369 · Cited by 1,528 · cited 1× · see citing works
“The main participants of pathways are proteins, present in different states referred to as proteoforms (Smith and Kelleher, 2013; Regnier and Kim, 2017).”
BackgroundHow many human proteoforms are there?
Aebersold, R., Agar, J. N., Amster, I. J., Baker, M. S., Bertozzi, C. R., Boja, E. S., Costello, C. E., Cravatt, B. F., Fenselau, C., Garcia, B. A., et al. (2018) · Nature Chemical Biology · doi:10.1038/nchembio.2576 · Cited by 907 · see citing works
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- Authors
- Burger, B., Hernández Sánchez, L. F., Lereim, R. R., Barsnes, H., & Vaudel, M.
- Affiliations
- University of Bergen (NO)
- Haukeland University Hospital (NO)
- Corresponding author
- Vaudel, Marc
- Venue
- Journal of Proteome Research
- Publisher
- openRxiv
- Published
- 2018-05-30
- Volume
- 17
- Issue
- 11
- Pages
- 3801-3809
- ISSN
- 1535-3893 (ISSN-L)
- OpenAlex
- W2892440169
- Cited by
- 3
- References
- 2
- Citations by year
- 2023: 1 · 2020: 1 · 2019: 1
- FWCI
- 0.18
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by
- Locations
- Journal of Proteome Research (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- NORA - Norwegian Open Research Archives (submittedVersion, other-oa)
- Funders
- Norges Forskningsråd
- Bergens Forskningsstiftelse
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- metabolic pathways, Reactome, protein-protein interaction network, pathway analysis, proteomics data interpretation, functional annotation
- MeSH terms
- Humans, Lymphocytes, Computational Biology, Myeloid Cells, Protein Interaction Mapping, Databases, Protein, Proteomics, Knowledge Bases, Metabolic Networks and Pathways, Protein Interaction Maps
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