Online resources on gene networks containing human and animal data

Abstract

Gene networks are molecular genetic systems that en sure the formation of phenotypic characteristics of or ganisms (molecular, biochemical, structural, morpho logical, 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 struc tural and functional organization of gene networks accumulated in modern databases is extremely valu able. This review characterizes a number of Internet accessible 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 web resources 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 biologi cal 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 conclud ed that at the first step of the gene network recon struction it is important to form a full set of informa tion 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.Key words: systems biology; databases; gene networks; Internet.Генные сети -это молекулярногенетические системы, обеспечи вающие формирование фенотипических характеристик организ мов (молекулярных, биохимических, структурных, морфологиче ских, поведенческих и т. д.) на основе информации, закодирован ной в их геномах. Реконструкция генных сетей обеспечивает мето дическую основу современной системной биологии. Большую ценность представляет информация о структурнофункциональ ной организации генных сетей, накопленная в современных базах данных. В настоящем обзоре представлена характеристика интер нетдоступных 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, предло женный обзор...

Gene networks in a post-genomic era

“…); (4) negative and positive feedbacks stabilizing the parameters of the gene network at a certain level, or, on the contrary, deviating them from the initial value, providing a transition to a new functional state [2]. Reconstruction of gene networks and deciphering their connectivity structure provide methodological basis for modern systems biology [3]. this review (1) introduces the concepts of Gene networks and related terms used in the post-genomic era (Gene regulatory networks (GRNs), transcription regulatory networks (tRNs), protein-protein interaction (PPI) networks, associative gene networks, etc.…”