Glioblastoma gene network reconstruction and ontology analysis by online bioinformatics tools

Abstract

Glioblastoma is the most aggressive type of brain tumors resistant to a number of antitumor drugs. The problem of therapy and drug treatment course is complicated by extremely high heterogeneity in the benign cell populations, the random arrangement of tumor cells, and polymorphism of their nuclei. The pathogenesis of gliomas needs to be studied using modern cellular technologies, genome- and transcriptome-wide technologies of high-throughput sequencing, analysis of gene expression on microarrays, and methods of modern bioinformatics to find new therapy targets. Functional annotation of genes related to the disease could be retrieved based on genetic databases and cross-validated by integrating complementary experimental data. Gene network reconstruction for a set of genes (proteins) proved to be effective approach to study mechanisms underlying disease progression. We used online bioinformatics tools for annotation of gene list for glioma, reconstruction of gene network and comparative analysis of gene ontology categories. The available tools and the databases for glioblastoma gene analysis are discussed together with the recent progress in this field.

Research and analysis of genes associated with hereditary predisposition to Crohn's disease and reconstruction of the gene network using bioinformatics tools

“…GeneMANIA (https://genemania.org) and STRING-DB (https://string-db.org/) tools were used to reconstruct the gene network of interactions of genes associated with Crohn's disease. We had follow scheme of applications of online tools recently published in [5] for glioblastoma analysis. Results: The GO analysis revealed that the most significant categories for genes associated with Crohn's disease are signaling pathways mediated by tumor necrosis factor and caused by cytokines, as well as reactions to the drug and cytosolic processes.…”

Computer modeling of glioblastoma gene network and hub genes analysis

“…The pathogenesis of gliomas needs to be studied using modern technologies to find new therapy targets. For an object such as gliomas, it is necessary to conduct new studies based on modern cellular technologies, genome-wide technologies for high-throughput sequencing, and the integration of available information from international databases and genomic projects [2].…”

Gene network reconstruction and functional association studies for oncological diseases using online bioinformatics tools

“…Results: We reconstructed gene networks for series of oncological diseases -glioma, lymphoma, and Kaposi's sarcoma. The work on gene network models include glioma [2], Parkinson's disease [5], and metabolic syndrome [9]. The steps include collection of a list of genes associated with the development of the disease (e.g., Parkinson's disease), analyze gene ontology categories for such a list, and reconstruct the gene network.…”

“…For the key disease genes derived from the gene network structure analysis, drug search options are considered [5]. This approach has already been tested for teaching the course "Fundamentals of Bioinformatics and Databases Management" at the Sechenov University [1,2]. In many cases, it require advanced training, additional education in modern genomics technologies, such as high-throughput genomic and transcriptomic sequencing, data analysis, metagenome sequencing, non-coding RNA studies, Artificial Intelligence (AI) applications in medicine, which greatly expand the range of classical bioinformatics tasks [4].…”