vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJ17.310vavilov-1265Research ArticleСИСТЕМНАЯ БИОЛОГИЯ ЧЕЛОВЕКА И ЖИВОТНЫХHUMAN AND ANIMAL SYSTEMS BIOLOGYИнтернет-доступные информационные ресурсы по генным сетям, включающие данные по человеку и животнымOnline resources on gene networks containing human and animal dataИгнатьеваЕ. В.IgnatievaE. V.

Новосибирск.

Novosibirsk.

eignat@bionet.nsc.ruАфонниковД. А.AfonnikovD. A.

Новосибирск.

Novosibirsk.

КолчановН. А. KolchanovN. A.

Новосибирск.

Novosibirsk.

Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университет.РоссияInstitute of Cytology and Genetics SB RAS; Novosibirsk State University.Russian Federation201720012018218895902Copyright © Игнатьева Е.В., Афонников Д.А., Колчанов Н.А., 20182018Игнатьева Е.В., Афонников Д.А., Колчанов Н.А.Ignatieva E.V., Afonnikov D.A.,  Kolchanov N.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/1265

Генные сети – это молекулярно­генетические системы, обеспечивающие формирование фенотипических характеристик организ­ мов (молекулярных, биохимических, структурных, морфологических, поведенческих и т. д.) на основе информации, закодированной в их геномах. Реконструкция генных сетей обеспечивает методическую основу современной системной биологии. Большую ценность представляет информация о структурно­функциональной организации генных сетей, накопленная в современных базах данных. В настоящем обзоре представлена характеристика интернет­доступных информационных ресурсов, ориентированных на человека и животных и содержащих данные по генным сетям и их функциональным модулям. Не претендуя на полноту охвата абсолютно всех информационных ресурсов, содержащих данные, относящиеся к человеку и животным по этой тематике, предложенный обзор создан для того, чтобы оценить современное состояние проблемы, а также представить критерии, согласно которым целесообразно оценивать полезность информационных ресурсов для конкретных исследовательских задач. Исходя из этого нами, во­первых, была сформирована и охарактеризована подборка баз данных, содержащих сведения о метаболических и сигнальных путях, а также о путях регуляции биологических процессов на клеточном и организменном уровнях. Во­вторых, в качестве примера описаны несколько известных баз данных по меж молекулярным взаимодействиям различных типов. В обзоре рас сматриваются следующие характеристики баз данных: 1) типы на копленной информации; 2) способы представления информации; 3) способы наполнения баз данных; 4) основные источники инфор мации; 5) программные средства, позволяющие осуществлять поиск и анализ данных. Сопоставление перечисленных характеристик показало, что рассмотренные базы данных очень гетерогенны по тематике, источникам, типам и способу представления информации, а также по возможностям формировать запросы и анализировать данные. Делается вывод о том, что до начала реконструкции генной сети определенного биологического процесса очень важно иметь пред ставление о максимально полном наборе информационных источников, из которых может быть взята информация. Приведены примеры веб­порталов, аккумулирующих сведения о базах данных и информационных ресурсах, которые могут быть полезны для реконструкции и анализа генных сетей.

Gene networks are molecular genetic systems that ensure the formation of phenotypic characteristics of organisms (molecular, biochemical, structural, morphological, behavioral, etc.) based on  information encoded in their genomes. Reconstruction of gene networks provides a methodological basis for modern systems biology. In this regard, the information on the structural and functional organization of gene networks accumulated in modern databases is extremely valuable. This review characterizes a number of Internetaccessible information resources oriented to humans and animals and containing data on gene networks and their functional modules. Without pretending to fully cover all information resources containing data related to humans and animals on the subject, the current review was created to report the current status of the problem and to present the criteria according to which we propose to evaluate the utility of webresources for specific research tasks. On this basis, we compiled and characterized a collection of databases containing information on metabolic and signaling pathways, as well as pathways of regulation of biological processes at the cellular and organismal levels. In addition, we observed the characteristics of several well­known databases containing data on interactions between biomolecules of various types. The following characteristics of databases were considered: (1) the types of information accumulated in the databases; (2) methods of data presentation; (3) methods of data collection; (4) data sources; (5) special search tools and options for data analysis. A comparison of the above characteristics showed that the databases are very heterogeneous according to their scopes, sources and types of data, interfaces, as well as according to their search options and data analysis tools. It was concluded that at the first step of the gene network reconstruction it is important to form a full set of information resources from which the data can be obtained. The web portals accumulating information about the databases that may be useful for the reconstruction and analysis of gene networks are specified.

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