TY - JOUR

T1 - RatDEGdb: a knowledge base of differentially expressed genes in the rat as a model object in biomedical research

AU - Chadaeva, I V

AU - Filonov, S V

AU - Zolotareva, K A

AU - Khandaev, B M

AU - Ershov, N I

AU - Podkolodnyy, N L

AU - Kozhemyakina, R V

AU - Rasskazov, D A

AU - Bogomolov, A G

AU - Kondratyuk, E Yu

AU - Klimova, N V

AU - Shikhevich, S G

AU - Ryazanova, M A

AU - Fedoseeva, L A

AU - Redina, О Е

AU - Kozhevnikova, O S

AU - Stefanova, N A

AU - Kolosova, N G

AU - Markel, A L

AU - Ponomarenko, M P

AU - Oshchepkov, D Yu

N1 - The authors are grateful to the Multi-Access Center “Bioinformatics” for access to computing resources under Project FWNR-2022-0020 and the Multi-Access Center “Conventional Animal Facility” for access to animals under Projects FWNR-2022-0019 and FWNR-2022-0015. Copyright © AUTHORS. Публикация для корректировки.

PY - 2023/12

Y1 - 2023/12

N2 - The animal models used in biomedical research cover virtually every human disease. RatDEGdb, a knowledge base of the differentially expressed genes (DEGs) of the rat as a model object in biomedical research is a collection of published data on gene expression in rat strains simulating arterial hypertension, age-related diseases, psychopathological conditions and other human afflictions. The current release contains information on 25,101 DEGs representing 14,320 unique rat genes that change transcription levels in 21 tissues of 10 genetic rat strains used as models of 11 human diseases based on 45 original scientific papers. RatDEGdb is novel in that, unlike any other biomedical database, it offers the manually curated annotations of DEGs in model rats with the use of independent clinical data on equal changes in the expression of homologous genes revealed in people with pathologies. The rat DEGs put in RatDEGdb were annotated with equal changes in the expression of their human homologs in affected people. In its current release, RatDEGdb contains 94,873 such annotations for 321 human genes in 836 diseases based on 959 original scientific papers found in the current PubMed. RatDEGdb may be interesting first of all to human geneticists, molecular biologists, clinical physicians, genetic advisors as well as experts in biopharmaceutics, bioinformatics and personalized genomics. RatDEGdb is publicly available at https://www.sysbio.ru/RatDEGdb.

AB - The animal models used in biomedical research cover virtually every human disease. RatDEGdb, a knowledge base of the differentially expressed genes (DEGs) of the rat as a model object in biomedical research is a collection of published data on gene expression in rat strains simulating arterial hypertension, age-related diseases, psychopathological conditions and other human afflictions. The current release contains information on 25,101 DEGs representing 14,320 unique rat genes that change transcription levels in 21 tissues of 10 genetic rat strains used as models of 11 human diseases based on 45 original scientific papers. RatDEGdb is novel in that, unlike any other biomedical database, it offers the manually curated annotations of DEGs in model rats with the use of independent clinical data on equal changes in the expression of homologous genes revealed in people with pathologies. The rat DEGs put in RatDEGdb were annotated with equal changes in the expression of their human homologs in affected people. In its current release, RatDEGdb contains 94,873 such annotations for 321 human genes in 836 diseases based on 959 original scientific papers found in the current PubMed. RatDEGdb may be interesting first of all to human geneticists, molecular biologists, clinical physicians, genetic advisors as well as experts in biopharmaceutics, bioinformatics and personalized genomics. RatDEGdb is publicly available at https://www.sysbio.ru/RatDEGdb.

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85181521091&origin=inward&txGid=8196df79b46584c3ee6c92b0d4cd939b

U2 - 10.18699/VJGB-23-92

DO - 10.18699/VJGB-23-92

M3 - Article

C2 - 38213701

VL - 27

SP - 794

EP - 806

JO - Вавиловский журнал генетики и селекции

JF - Вавиловский журнал генетики и селекции

SN - 2500-0462

IS - 7

ER -