Russian Journal of Biological Physics and Chemisrty Russian Journal of Biological Physics and Chemisrty АКТУАЛЬНЫЕ ВОПРОСЫ БИОЛОГИЧЕСКОЙ ФИЗИКИ И ХИМИИ 2499-9962 83713 10.29039/rusjbpc.2023.0647 МЕДИЦИНСКАЯ БИОФИЗИКА И БИОФИЗИЧЕСКАЯ ХИМИЯ MEDICAL BIOPHYSICS AND BIOPHYSICAL CHEMISTRY МЕДИЦИНСКАЯ БИОФИЗИКА И БИОФИЗИЧЕСКАЯ ХИМИЯ RECONSTRUCTION OF GENE AND ASSOCIATIVE NETWORKS OF DISEASES TO SEARCH FOR TARGET GENES РЕКОНСТРУКЦИЯ ГЕННЫХ И АССОЦИАТИВНЫХ СЕТЕЙ ЗАБОЛЕВАНИЙ ДЛЯ ПОИСКА ГЕНОВ-МИШЕНЕЙ Туркина В. А. Turkina V. A. vasundel@mail.ru Ярема П. О. Iarema P. O. Майорова А. А. Mayorova A. A. Орлова Н. Г. Orlova N. G. Савина Е. А. Savina E. A. Орлов Юрий Львович Orlov Yuriy L'vovich orlov@d-health.institute

доктор биологических наук;

doctor of sciences in biology;

 Первый МГМУ им. И.М. Сеченова Минздрава России (Сеченовский Университет) Москва Россия Sechenov University Moscow Russian Federation Первый МГМУ им. И.М. Сеченова Минздрава России (Сеченовский Университет) Москва Россия Sechenov University Moscow Russian Federation Первый МГМУ им. И.М. Сеченова Минздрава России (Сеченовский Университет) Москва Россия Sechenov University Moscow Russian Federation Финансовый Университет при Правительстве РФ Москва Россия Financial University under the Government of the Russian Federation Moscow Russian Federation Первый МГМУ им. И.М. Сеченова Минздрава России (Сеченовский Университет) Москва Россия Sechenov University Moscow Russian Federation Институт молекулярной биологии имени В.А. Энгельгардта РАН Москва Россия Engelhardt Institute of Molecular Biology of RAS Moscow Russian Federation Первый МГМУ им. И.М. Сеченова Минздрава России (Сеченовский Университет) Москва Россия Sechenov University Moscow Russian Federation Институт цитологии и генетики СО РАН Новосибирск Россия Institute of Cytology and Genetics SB RAS Novosibirsk Russian Federation Новосибирский государственный университет Новосибирск Россия Novosibirsk State University Novosibirsk Russian Federation Российский университет дружбы народов Peoples’ Friendship University of Russia 06 06 2024 06 06 2024 8 4 458 467 10 08 2023 https://rusjbpc.ru/en/nauka/article/83713/view

Компьютерная реконструкция генных сетей – наборов взаимодействующих макромолекул, объединенных общей функцией – представляет собой комплексную задачу биоинформатики. Генные сети как графические структуры представляют удобное средство визуализации, дают качественно новую информацию о наборе исследуемых генов, описание их биологических функций. В более широком плане мы рассматриваем ассоциативные генные сети заболеваний, куда входят не только гены и их продукты – белки, метаболиты, некодирующие РНК, лекарственные соединения, но и общие признаки заболеваний – симптомы, фенотипические проявления. Программные инструменты для компьютерной реконструкции графа генной сети активно развиваются в мире, используются в биомедицине. Мы рассматриваем онлайн-доступные инструменты биоинформатики для реконструкции генных сетей по списку генов и соответствующий компьютерный конвейер обработки данных. Анализ структуры генной сети заболевания позволяет выделить узловые гены, как мишени для терапии. Рассмотрены примеры применения онлайн-программ для анализа генной сети глиомы. Предложенный подход может быть масштабирован на другие функциональные наборы генов, связанные с заболеваниями человека. Используя подобные подходы биоинформатики, рассматривались генные сети комплексных заболеваний, таких как болезнь Паркинсона, деменция, шизофрения, рак молочной железы и другие виды рака.

Computer reconstruction of gene networks—sets of interacting macromolecules with common functions – is a complex task in bioinformatics. Gene networks, presented as graphical structures, offer a convenient means of visualization and provide qualitatively new insights into the set of studied genes and their biological functions. Expanding further, we explore associative gene networks related to diseases. These networks encompass not only genes and their products (proteins, metabolites, non-coding RNA and drug compounds) but also common disease indicators (symptoms, phenotypic manifestations). Software tools aimed at reconstructing gene network graphs are undergoing active development worldwide and find significant utility in biomedicine. We evaluate available online bioinformatics tools for gene network reconstruction based on gene lists and corresponding computer analysis pipelines. We delve into examples showcasing the utilization of online programs for analyzing the glioma gene network. The proposed approach can be extended to other functional gene sets linked to diseases. Scrutinizing the structure of disease-associated gene networks enables the identification of pivotal genes, which can serve as therapeutic targets. Employing similar bioinformatics strategies, gene networks of intricate disorders such as Parkinson's disease, dementia, schizophrenia, breast cancer, and other cancers have been explored. We delve into the applications of computer programs for gene network analysis and address pedagogical aspects of the field.

 биоинформатика генные сети глиома комплексные заболевания белок-белковые взаимодействия медицинская информатика bioinformatics gene networks glioma complex diseases protein-protein interactions medical informatics Работа поддержана грантом бюджетным проектов ИЦиГ СО РАН FWNR-2022-0020 "Системная биология и биоинформатика: реконструкция, анализ и моделирование структурно-функциональной организации и эволюции генных сетей человека, животных, растений и микроорганизмов".

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