Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090, Russia.
BMC Bioinformatics. 2019 Feb 5;20(Suppl 1):34. doi: 10.1186/s12859-018-2567-6.
Consideration of tissue-specific gene expression in reconstruction and analysis of molecular genetic networks is necessary for a proper description of the processes occurring in a specified tissue. Currently, there are a number of computer systems that allow the user to reconstruct molecular-genetic networks using the data automatically extracted from the texts of scientific publications. Examples of such systems are STRING, Pathway Commons, MetaCore and Ingenuity. The MetaCore and Ingenuity systems permit taking into account tissue-specific gene expression during the reconstruction of gene networks. Previously, we developed the ANDSystem tool, which also provides an automated extraction of knowledge from scientific texts and allows the reconstruction of gene networks. The main difference between our system and other tools is in the different types of interactions between objects, which makes the ANDSystem complementary to existing well-known systems. However, previous versions of the ANDSystem did not contain any information on tissue-specific expression.
A new version of the ANDSystem has been developed. It offers the reconstruction of associative gene networks while taking into account the tissue-specific gene expression. The ANDSystem knowledge base features information on tissue-specific expression for 272 tissues. The system allows the reconstruction of combined gene networks, as well as performing the filtering of genes from such networks using the information on their tissue-specific expression. As an example of the application of such filtering, the gene network of the extrinsic apoptotic signaling pathway was analyzed. It was shown that considering different tissues can lead to changes in gene network structure, including changes in such indicators as betweenness centrality of vertices, clustering coefficient, network centralization, network density, etc. CONCLUSIONS: The consideration of tissue specificity can play an important role in the analysis of gene networks, in particular solving the problem of finding the most significant central genes. Thus, the new version of ANDSystem can be employed for a wide range of tasks related to biomedical studies of individual tissues. It is available at http://www-bionet.sscc.ru/and/cell /.
在重建和分析分子遗传网络时，考虑组织特异性基因表达对于正确描述特定组织中发生的过程是必要的。目前，有许多计算机系统允许用户使用从科学出版物文本中自动提取的数据来重建分子遗传网络。例如 STRING、Pathway Commons、MetaCore 和 Ingenuity 等系统。MetaCore 和 Ingenuity 系统允许在重建基因网络时考虑组织特异性基因表达。此前，我们开发了 ANDSystem 工具，该工具还提供了从科学文本中自动提取知识的功能，并允许重建基因网络。我们的系统与其他工具的主要区别在于对象之间的交互类型不同，这使得 ANDSystem 与现有的知名系统互补。然而，之前版本的 ANDSystem 不包含任何组织特异性表达的信息。
我们开发了 ANDSystem 的新版本。它提供了在考虑组织特异性基因表达的情况下，对关联基因网络进行重建的功能。ANDSystem 知识库包含了 272 种组织的组织特异性表达信息。该系统允许重建组合基因网络，并使用其组织特异性表达信息对这些网络中的基因进行过滤。作为这种过滤应用的一个例子，我们分析了外在凋亡信号通路的基因网络。结果表明，考虑不同的组织可以导致基因网络结构发生变化，包括改变顶点的介数中心性、聚类系数、网络集中化、网络密度等指标。
考虑组织特异性可以在基因网络分析中发挥重要作用，特别是在解决寻找最重要的中心基因的问题上。因此，新版本的 ANDSystem 可以用于与单个组织的生物医学研究相关的广泛任务。该系统可在 http://www-bionet.sscc.ru/and/cell/ 上获得。
