Glioblastoma gene network reconstruction and ontology analysis by online bioinformatics tools.

Natalya V Gubanova,Nina G Orlova,Yuriy L Orlov,Arthur I Dergilev,Nina Y Oparina

doi:10.1515/jib-2021-0031

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.

Highlights

Glioblastomas, along with astrocytomas, are the most common primary tumors of the central nervous system and make up approximately 60–70% of all pure brain tumors, challenging search for new therapy methods
The Allen Institute has developed the Ivy Glioblastoma Atlas Project database according to patients with glioma. We demonstrate that these publicly available online bioinformatics tools can give helpful information for annotation of gene list for glioblastoma, reconstruction of gene network and comparative analysis of the related diseases
We have analyzed gene ontology categories for the same gene list obtained by different online bioinformatics tools

Summary

Introduction

Glioblastomas, along with astrocytomas, are the most common primary tumors of the central nervous system and make up approximately 60–70% of all pure brain tumors, challenging search for new therapy methods. Tumors of the brain and spinal cord are the second most common form of malignancy in children after leukemia [4]. Glioblastoma has higher burden in survival of the patients with malignant brain tumors [5]. Gliomas are the most common heterogeneous group of malignant tumors of the brain among the adult population, which differ in morphological characteristics, clinical course, and response to radio- and chemotherapy. In the treatment of glioblastoma with drugs, an obstacle is its resistance to a number of antitumor drugs initially, as well as the presence of a blood-brain barrier that negates the effectiveness of most chemotherapeutic agents and targeted drugs [3, 6]

Methods

Results

Conclusion