ArticlePhysiological genomics2017
Data integration in physiology using Bayes' rule and minimum Bayes' factors: deubiquitylating enzymes in the renal collecting duct.
Article in Physiological genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 17 citations in OpenAlex.
- Utilizing Omic Data to Understand Integrative Physiology.Physiology (Bethesda, Md.) · 2025Review
- Proximity-dependent biotinylation reveals an interaction between ubiquitin-specific peptidase 46 and centrosome-related proteins.FEBS open bio · 2025Article
- OTUB1 regulation of ferroptosis and the protective role of ferrostatin-1 in lupus nephritis.Cell death & disease · 2024Article
- Bayesian mapping of protein kinases to vasopressin-regulated phosphorylation sites in renal collecting duct.American journal of physiology. Renal physiology · 2024Article
- Enzyme Databases in the Era of Omics and Artificial Intelligence.International journal of molecular sciences · 2023Review
- Bayesian analysis of dynamic phosphoproteomic data identifies protein kinases mediating GPCR responses.Cell communication and signaling : CCS · 2022Article
- Systems Biology of the Vasopressin V2 Receptor: New Tools for Discovery of Molecular Actions of a GPCR.Annual review of pharmacology and toxicology · 2022Review
- Bayesian identification of candidate transcription factors for the regulation ofAmerican journal of physiology. Renal physiology · 2021Article
- Phosphoproteomic Identification of Vasopressin/cAMP/Protein Kinase A-Dependent Signaling in Kidney.Molecular pharmacology · 2021Review
- Deep Proteomic Deconvolution of Interferons and HBV Transfection Effects on a Hepatoblastoma Cell Line.ACS omega · 2020Article
- Genome-Wide Mapping of DNA Accessibility and Binding Sites for CREB and C/EBPJournal of the American Society of Nephrology : JASN · 2018Article
- Identification of β-catenin-interacting proteins in nuclear fractions of native rat collecting duct cells.American journal of physiology. Renal physiology · 2017Article
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
A major challenge in physiology is to exploit the many large-scale data sets available from "-omic" studies to seek answers to key physiological questions. In previous studies, Bayes' theorem has been used for this purpose. This approach requires a means to map continuously distributed experimental data to probabilities (likelihood values) to derive posterior probabilities from the combination of prior probabilities and new data. Here, we introduce the use of minimum Bayes' factors for this purpose and illustrate the approach by addressing a physiological question, "Which deubiquitylating enzymes (DUBs) encoded by mammalian genomes are most likely to regulate plasma membrane transport processes in renal cortical collecting duct principal cells?" To do this, we have created a comprehensive online database of 110 DUBs present in the mammalian genome (https://hpcwebapps.cit.nih.gov/ESBL/Database/DUBs/). We used Bayes' theorem to integrate available information from large-scale data sets derived from proteomic and transcriptomic studies of renal collecting duct cells to rank the 110 known DUBs with regard to likelihood of interacting with and regulating transport processes. The top-ranked DUBs were OTUB1, USP14, PSMD7, PSMD14, USP7, USP9X, OTUD4, USP10, and UCHL5. Among these USP7, USP9X, OTUD4, and USP10 are known to be involved in endosomal trafficking and have potential roles in endosomal recycling of plasma membrane proteins in the mammalian cortical collecting duct.
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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.