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      VARIDT 3.0: the phenotypic and regulatory variability of drug transporter

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          Abstract

          The phenotypic and regulatory variability of drug transporter (DT) are vital for the understanding of drug responses, drug-drug interactions, multidrug resistances, and so on. The ADME property of a drug is collectively determined by multiple types of variability, such as: microbiota influence (MBI), transcriptional regulation (TSR), epigenetics regulation (EGR), exogenous modulation (EGM) and post-translational modification (PTM). However, no database has yet been available to comprehensively describe these valuable variabilities of DTs. In this study, a major update of VARIDT was therefore conducted, which gave 2072 MBIs, 10 610 TSRs, 46 748 EGRs, 12 209 EGMs and 10 255 PTMs. These variability data were closely related to the transportation of 585 approved and 301 clinical trial drugs for treating 572 diseases. Moreover, the majority of the DTs in this database were found with multiple variabilities, which allowed a collective consideration in determining the ADME properties of a drug. All in all, VARIDT 3.0 is expected to be a popular data repository that could become an essential complement to existing pharmaceutical databases, and is freely accessible without any login requirement at: https://idrblab.org/varidt/.

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          NCBI GEO: archive for functional genomics data sets—update

          Tanya Barrett, Stephen Wilhite, Pierre Ledoux … (2012)
          The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats. GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data. This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data.
          Article 0 comments Cited 2456 times – based on 0 reviews     Review now
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            DrugBank 5.0: a major update to the DrugBank database for 2018

            David S Wishart, Yannick D Feunang, An C Guo … (2017)
            Abstract DrugBank (www.drugbank.ca) is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. First described in 2006, DrugBank has continued to evolve over the past 12 years in response to marked improvements to web standards and changing needs for drug research and development. This year’s update, DrugBank 5.0, represents the most significant upgrade to the database in more than 10 years. In many cases, existing data content has grown by 100% or more over the last update. For instance, the total number of investigational drugs in the database has grown by almost 300%, the number of drug-drug interactions has grown by nearly 600% and the number of SNP-associated drug effects has grown more than 3000%. Significant improvements have been made to the quantity, quality and consistency of drug indications, drug binding data as well as drug-drug and drug-food interactions. A great deal of brand new data have also been added to DrugBank 5.0. This includes information on the influence of hundreds of drugs on metabolite levels (pharmacometabolomics), gene expression levels (pharmacotranscriptomics) and protein expression levels (pharmacoprotoemics). New data have also been added on the status of hundreds of new drug clinical trials and existing drug repurposing trials. Many other important improvements in the content, interface and performance of the DrugBank website have been made and these should greatly enhance its ease of use, utility and potential applications in many areas of pharmacological research, pharmaceutical science and drug education.
            Article 0 comments Cited 2156 times – based on 0 reviews     Review now
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              affy--analysis of Affymetrix GeneChip data at the probe level.

              L. Gautier, L. Cope, B Bolstad … (2004)
              The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used. The affy package is an R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. The package is currently in its second release, affy provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data. In this paper, we present the main classes and functions in the package and demonstrate how they can be used to process probe-level data. We also demonstrate the importance of probe-level analysis when using the Affymetrix GeneChip platform.
              Article 0 comments Cited 801 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Jiayi Yin
                Zhen Chen
                Nanxin You
                Fengcheng Li
                Hanyu Zhang:
                ORCID: https://orcid.org/0000-0002-4728-7702
                Jia Xue
                Hui Ma
                Qingwei Zhao
                Lushan Yu
                Su Zeng:
                ORCID: https://orcid.org/0000-0002-1418-6825
                Feng Zhu:
                ORCID: https://orcid.org/0000-0001-8069-0053
                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: 05 January 2024
                Publication date (Electronic): 11 October 2023
                Publication date PMC-release: 11 October 2023
                Volume: 52
                Issue: D1
                Pages: D1490-D1502
                Affiliations
                College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University , Hangzhou 310058, China
                Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou 330110, China
                College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University , Hangzhou 310058, China
                College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University , Hangzhou 310058, China
                College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University , Hangzhou 310058, China
                The Children's Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou 310052, China
                College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University , Hangzhou 310058, China
                College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University , Hangzhou 310058, China
                College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University , Hangzhou 310058, China
                College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University , Hangzhou 310058, China
                College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University , Hangzhou 310058, China
                College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University , Hangzhou 310058, China
                College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University , Hangzhou 310058, China
                Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou 330110, China
                Author notes
                To whom correspondence should be addressed. Tel: +86 189 8946 6518; Fax: +86 571 8820 8444; Email: zhufeng@ 123456zju.edu.cn
                Correspondence may also be addressed to Su Zeng. Email: zengsu@ 123456zju.edu.cn
                Correspondence may also be addressed to Lushan Yu. Email: yuls@ 123456zju.edu.cn

                The authors wish it to be known that, in their opinion, the first four authors should be regarded as Joint First Authors.

                Author information
                https://orcid.org/0000-0002-4728-7702
                https://orcid.org/0000-0002-1418-6825
                https://orcid.org/0000-0001-8069-0053
                Article
                Publisher ID: gkad818
                DOI: 10.1093/nar/gkad818
                PMC ID: 10767864
                PubMed ID: 37819041
                SO-VID: e21a5894-b022-4ad8-9782-fddccda57563
                Copyright © © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                Date accepted : 27 September 2023
                Date revision received : 01 September 2023
                Date received : 25 July 2023
                Page count
                Pages: 13
                Funding
                Funded by: National Natural Science Foundation of China, DOI 10.13039/501100001809;
                Award ID: 82373790
                Award ID: 22220102001
                Award ID: U1909208
                Award ID: 81872798
                Funded by: Natural Science Foundation of Zhejiang Province, DOI 10.13039/501100004731;
                Award ID: LR21H300001
                Funded by: National Key R&D Program of China, DOI 10.13039/501100012166;
                Award ID: 2022YFC3400501
                Funded by: Leading Talent of the ‘Ten Thousand Plan’ National High-Level Talents Special Support Plan of China;
                Funded by: The Double Top-Class Universities;
                Award ID: 181201*194232101
                Funded by: Fundamental Research Funds for Central Universities;
                Award ID: 2018QNA7023
                Funded by: Key R&D Program of Zhejiang Province, DOI 10.13039/100022963;
                Award ID: 2020C03010
                Funded by: Westlake Laboratory (Westlake Laboratory of Life Science & Biomedicine); Alibaba Cloud; Information Technology Center of Zhejiang University;
                Funded by: Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare;
                Award ID: LR21H300001
                Categories
                Subject: AcademicSubjects/SCI00010
                Subject: Database Issue

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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