vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJGB-23-92vavilov-3979Research ArticleСИСТЕМНАЯ КОМПЬЮТЕРНАЯ БИОЛОГИЯSYSTEMS COMPUTATIONAL BIOLOGYБаза знаний RatDEGdb по дифференциально экспрессирующимся генам крысы как модельного объекта биомедицинских исследованийRatDEGdb: a knowledge base of differentially expressed genes in the rat as a model object in biomedical researchhttps://orcid.org/0000-0002-2724-5441ЧадаеваИ. В.ChadaevaI. V.

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ФилоновС. В.FilonovS. V.

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ЗолотареваК. А.ZolotarevaK. A.

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ХандаевБ. М.KhandaevB. M.

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https://orcid.org/0000-0003-3423-3497ЕршовН. И.ErshovN. I.

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https://orcid.org/0000-0001-9132-7997ПодколодныйН. Л.PodkolodnyyN. L.

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https://orcid.org/0000-0001-8948-1127КожемякинаР. В.KozhemyakinaR. V.

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https://orcid.org/0000-0003-4795-0954РассказовД. А.RasskazovD. A.

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https://orcid.org/0000-0003-4359-6089БогомоловА. Г.BogomolovA. G.

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https://orcid.org/0000-0001-8672-7216КондратюкЕ. Ю.KondratyukE. Yu.

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р.п. Краснообск, Новосибирская область

 

Krasnoobsk, Novosibirsk region

КлимоваН. В.KlimovaN. V.

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ШихевичС. Г.ShikhevichS. G.

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РязановаМ. А.RyazanovaM. A. 

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ФедосееваЛ. А.FedoseevaL. A.

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https://orcid.org/0000-0003-0942-8460РединаО. Е.RedinaО. Е.

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https://orcid.org/0000-0001-6475-4061КожевниковаО. С.KozhevnikovaО. S.

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https://orcid.org/0000-0001-5127-5993СтефановаН. А.StefanovaN. A.

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https://orcid.org/0000-0003-2398-8544КолосоваН. Г.KolosovaN. G.

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https://orcid.org/0000-0002-1550-1647МаркельА. Л.MarkelA. L.

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https://orcid.org/0000-0003-1663-318XПономаренкоМ. П.PonomarenkoM. P.

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pon@bionet.nsc.ruhttps://orcid.org/0000-0002-6097-5155ОщепковД. Ю.OshchepkovYu. D.

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Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университетРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State UniversityRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университетРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Институт вычислительной математики и математической геофизики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Institute of Computational Mathematics and Mathematical Geophysics of the Siberian Branch of the Russian Academy of SciencesRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Сибирский федеральный научный центр агробиотехнологий Российской академии наукРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of SciencesRussian Federation202311122023277794806Copyright © Чадаева И.В., Филонов С.В., Золотарева К.А., Хандаев Б.М., Ершов Н.И., Подколодный Н.Л., Кожемякина Р.В., Рассказов Д.А., Богомолов А.Г., Кондратюк Е.Ю., Климова Н.В., Шихевич С.Г., Рязанова М.А., Федосеева Л.А., Редина О.Е., Кожевникова О.С., Стефанова Н.А., Колосова Н.Г., Маркель А.Л., Пономаренко М.П., Ощепков Д.Ю., 20232023Чадаева И.В., Филонов С.В., Золотарева К.А., Хандаев Б.М., Ершов Н.И., Подколодный Н.Л., Кожемякина Р.В., Рассказов Д.А., Богомолов А.Г., Кондратюк Е.Ю., Климова Н.В., Шихевич С.Г., Рязанова М.А., Федосеева Л.А., Редина О.Е., Кожевникова О.С., Стефанова Н.А., Колосова Н.Г., Маркель А.Л., Пономаренко М.П., Ощепков Д.Ю.Chadaeva I.V., Filonov S.V., Zolotareva K.A., Khandaev B.M., Ershov N.I., Podkolodnyy N.L., Kozhemyakina R.V., Rasskazov D.A., Bogomolov A.G., Kondratyuk E.Y., Klimova N.V., Shikhevich S.G., Ryazanova M.A., Fedoseeva L.A., Redina О.Е., Kozhevnikova О.S., Stefanova N.A., Kolosova N.G., Markel A.L., Ponomarenko M.P., Oshchepkov Y.D.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/3979

Животные модели, используемые в биомедицинских исследованиях, в настоящее время охватывают практически весь известный спектр заболеваний человека. База знаний RatDEGdb по дифференциально экспрессирующимся генам (ДЭГ) крысы как модельного объекта в биомедицинских исследованиях представляет собой коллекцию опубликованных данных по экспрессии генов у крыс разных линий, предназначенных для изучения артериальной гипертонии, болезней пожилого возраста, психопатологических состояний и других заболеваний человека. Текущий выпуск RatDEGdb содержит 25 101 ДЭГ, представляющих 14 320 уникальных генов крысы, которые изменяют уровень транскрипции в 21 ткани 10 генетических линий крысы в качестве моделей 11 заболеваний человека согласно 45 оригинальным научным статьям. Новшество RatDEGdb по сравнению с другими биомедицинскими базами данных заключается в курируемой аннотации отклонений ДЭГ крысы как модельного объекта с использованием независимых клинических данных об однонаправленных изменениях экспрессии гомологичных генов, выявленных у людей при различных патологиях. Собранные ДЭГ крыс были аннотированы однонаправленными изменениями экспрессии гомологичных им генов человека у больных людей относительно здоровых. К настоящему времени выпуск RatDEGdb содержит 94 873 такие аннотации для 321 гена человека при 836 заболеваниях согласно 959 оригинальным научным статьям, найденным в текущем выпуске базы данных PubMed. Представленная база знаний может быть интересна в первую очередь специалистам по генетике человека, молекулярным биологам, клиницистам и генетическим консультантам, а также специалистам в области биофармацевтики, биоинформатики и персонализированной геномики. RatDEGdb является общедоступной  (https://www.sysbio.ru/RatDEGdb).

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.

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The authors declare that there are no conflicts of interest present.