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The laboratory rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have relevance to human physiology and disease. The Rat Genome Database (RGD, http://rgd.mcw.edu ) is a model organism database that provides access to a wide variety of curated rat data including disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components for genes, quantitative trait loci, and strains. We present an overview of the database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the rat.
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http://dx.doi.org/10.1007/978-1-4939-7737-6_8 | DOI Listing |
Genome Biol
September 2025
Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
Background: Recent advances in high-throughput sequencing technologies have enabled the collection and sharing of a massive amount of omics data, along with its associated metadata-descriptive information that contextualizes the data, including phenotypic traits and experimental design. Enhancing metadata availability is critical to ensure data reusability and reproducibility and to facilitate novel biomedical discoveries through effective data reuse. Yet, incomplete metadata accompanying public omics data may hinder reproducibility and reusability and limit secondary analyses.
View Article and Find Full Text PDFJ Hum Genet
September 2025
Division of Integrative Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Comprehensive genomic profiling (CGP) expands treatment options for solid tumor patients and identifies hereditary cancers. However, in Japan, confirmatory tests have been conducted in only 31.6% of patients with presumed germline pathogenic variants (GPVs) detected through tumor-only testing.
View Article and Find Full Text PDFChem Res Toxicol
September 2025
University of Texas Medical Branch, Galveston, Texas 77555, United States.
Glioblastoma (GBM) is a lethal brain tumor with limited therapeutic options. Temozolomide (TMZ), a standard-of-care chemotherapeutic agent, exerts its cytotoxicity by alkylating DNA, which triggers a DNA damage response and depletes ATP and NAD. However, TMZ also releases the byproduct 4-amino-5-imidazole carboxamide (AIC), which is believed to be a benign metabolite.
View Article and Find Full Text PDFSci Total Environ
September 2025
Department of Orthopedics and Traumatology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, Sichuan Province, China. Electronic address:
The objective of this research was to use a network toxicology approach to examine the possible toxicity of the cigarette toxicants nicotine and coal tar that cause osteoporosis (OP) as well as its molecular processes. We determined the primary chemical structures and 128 targets of action of tar and nicotine using the Swiss Target Prediction, NP-MRD, and PubChem databases. We discovered that genes including DNAJB1, CCDC8, LINC00888, ATP6V1G1, MPV17L2, PPCS, and TACC1 had a disease prognostic guiding value by LASSO analysis and differential analysis of GEO microarray data.
View Article and Find Full Text PDFBackground: A significant surge in pertussis cases since early 2023 has raised serious public health concerns. To investigate the potential mechanisms contributing to this increased prevalence, we collected throat swab specimens from children exhibiting pertussis symptoms and conducted detailed molecular characterization.
Methods: All Bordetella pertussis (B.