Motivation and Aim: Kaposi's sarcoma is a cancer that develops from cells that line the lymph or blood vessels [1]. It usually appears as tumors on the skin or mucosal surfaces (inside the mouth), but these tumors can also develop in other parts of the body, such as the lymph nodes (bean-sized clusters of immune cells throughout the body), the lungs, or the digestive tract. It is important to describe new target genes for this disease. We aimed reconstruct gene network for future development of novel therapeutics or repurposing of existing treatment strategies, particularly in identifying new biomarkers as hub genes in such network.
Methods and Algorithms:We used open bioinformatics tools and databases following the approaches for gene network reconstruction and analysis presented in [2,4]. The task is to build (collect) a list of genes associated with the development of Kaposi's sarcoma, analyze the categories of gene ontologies for such a list, and reconstruct the gene network. First, we constructed the list of genes associated with a hereditary predisposition to Kaposi's sarcoma. The Internet-resource OMIM (Online Mendelian Inheritance in Man) (https://omim.org/) was used to analyze the genes. A search for the keyword Kaposi sarcoma (Kaposi's sarcoma) gave 273 genes -ACTFS, ACTG2, ADSL, ALKBH1, etc. We used also GeneCards.org platform for the annotation of sarcoma genes. Next step is estimation of enriched gene ontologies categories in the gene list and gene network reconstruction. The PANTHER resources (Protein Analysis THrough Evolutionary Relationships) (http://pantherdb.org/) were used to analyze the categories of gene ontologies. Results: The most significant categories for Kaposi's sarcoma genes were regulation of metabolic processes of the connection of nitrogen and macromolecules, regulation of the cellular metabolic process, regulation of cell proliferation, regulation of the process of biosynthesis and the metabolic process of RNA. Next, the categories of gene ontologies for molecular functions were calculated. The most significant categories are heterocyclic binding, organic cyclic binding, protein binding, and to a lesser extent specific DNA binding. Further, similarly, with the help of PANTHER, an ontology table for cellular components was built. The most significant categories for Kaposi's sarcoma genes are the nucleoplasm, nucleus, nuclear chromosome, chromatin, intracellular non-membrane organelles (ribosomes). Thus, PANTHER for Kaposi's sarcoma genes confirm the categories of gene ontologies of protein binding, nuclei, non-membrane organelles, metabolic processes, and RNA biosynthesis. The most significant categories for this list of genes include the regulation of metabolic processes, cell proliferation, and transcriptional disruption in cancer.