ArticleNucleic acids research2006
The outcomes of pathway database computations depend on pathway ontology.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
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- Proteomic profiling of zinc homeostasis mechanisms inbioRxiv : the preprint server for biology · 2025Article
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- StandardizedFrontiers in pharmacology · 2023Article
- Analytical Considerations of Large-Scale Aptamer-Based Datasets for Translational Applications.Cancers · 2022Review
- Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics.BMC genomics · 2021Article
- From Genome to Drugs: New Approaches in Antimicrobial Discovery.Frontiers in pharmacology · 2021Review
- Pathway Analysis Integrating Genome-Wide and Functional Data Identifies PLCG2 as a Candidate Gene for Age-Related Macular Degeneration.Investigative ophthalmology & visual science · 2019Article
- SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases.Database : the journal of biological databases and curation · 2018Article
- A novel approach to select differential pathways associated with hypertrophic cardiomyopathy based on gene co‑expression analysis.Molecular medicine reports · 2017Article
- Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification.Oncotarget · 2016Article
- Pathway Analysis: State of the Art.Frontiers in physiology · 2015Review
- Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges.Database : the journal of biological databases and curation · 2015Review
- Pathway analysis of the human brain transcriptome in disease.Journal of molecular neuroscience : MN · 2013Review
- A systematic comparison of the MetaCyc and KEGG pathway databases.BMC bioinformatics · 2013Article
- Genetics and epigenetics of rheumatoid arthritis.Nature reviews. Rheumatology · 2013Review
- Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction.BMC bioinformatics · 2012Article
- The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes.PLoS computational biology · 2012Article
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2 authors.
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Abstract
Different biological notions of pathways are used in different pathway databases. Those pathway ontologies significantly impact pathway computations. Computational users of pathway databases will obtain different results depending on the pathway ontology used by the databases they employ, and different pathway ontologies are preferable for different end uses. We explore differences in pathway ontologies by comparing the BioCyc and KEGG ontologies. The BioCyc ontology defines a pathway as a conserved, atomic module of the metabolic network of a single organism, i.e. often regulated as a unit, whose boundaries are defined at high-connectivity stable metabolites. KEGG pathways are on average 4.2 times larger than BioCyc pathways, and combine multiple biological processes from different organisms to produce a substrate-centered reaction mosaic. We compared KEGG and BioCyc pathways using genome context methods, which determine the functional relatedness of pairs of genes. For each method we employed, a pair of genes randomly selected from a BioCyc pathway is more likely to be related by that method than is a pair of genes randomly selected from a KEGG pathway, supporting the conclusion that the BioCyc pathway conceptualization is closer to a single conserved biological process than is that of KEGG.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.