Browsing by Author "Basar, Md. Abul"

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A System Biology and Bioinformatics Approach to Determine the Molecular Signature, Core Ontologies, Functional Pathways, Drug Compounds in Between Stress and Type 2 Diabetes
(IEEE, 2023-06-29) Basar, Md. Abul; Hasan, Md. Rakibul; Paul, Bikash Kumar; Shadhin, Khairul Alam; Mollah, Md. Sarwar
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. It involves the analysis of large amounts of biological data, such as DNA sequences, protein structures, and gene expression patterns. Bioinformatics is used to develop new methods for understanding and analyzing biological data, as well as to develop new tools and technologies for biological research. Bioinformatics is used in a variety of fields, including genomics, proteomics, and drug discovery. In this study, focus on two severe diseases which affect millions of people globally such as stress and type 2 diabetes. Stress can have a significant impact on people with type 2 diabetes. Stress can cause blood sugar levels to rise, making it difficult to manage diabetes. The purpose of this research is to use various bioinformatics methods to discover potential therapeutic drugs and functional pathways between stress and type 2 diabetes. The microarray datasets GSE183648 and GSE20966 are used for the analysis of stress and type 2 diabetes samples respectively. After the datasets have been preprocessed and filtered through the use of the R programming language, identified the common DEGs. The depiction of common DEGs is shown by venn diagram. Next, the most active genes are identified through topological properties, and PPIs are built from the similar differential expressed genes (DEGs). These five genes NTRK2, SOCS3, NEDD9, MAP3K8, and SIRPA are the most important hub genes with in the interaction network of protein-protein. According to the common DEGs, GO terms molecular function (MF), KEGG and WikiPathways are shown in this study. Gene-miRNA interaction, TF-gene regulatory network, module analysis, GO terms (Biological Process, Cellular Component), Pathways (Reactome, BioCarta, BioPlanet) are all things that could be done with this research work in the future. In last, a therapeutic drug compounds are recommended on the basis of common DEGs.
Identification of Drug and Protein-Protein Interaction Network Among Stress and Depression: A Bioinformatics Approach
(Elsevier, 2023-01-18) Basar, Md. Abul; Hosen, Md. Faruk; Paul, Bikash Kumar; Hasan, Md. Rakibul; Shamim, S.M.; Bhuyian, Touhid
The fields of data mining, computational biology, and statistics have been combined to form the massive research area of bioinformatics. In the areas of genetics, education, and healthcare, bioinformatics integrates the tools available in different fields such as computing, inventorying, performing statistical analyses, and collecting and processing genomic data. Stress and depression are two of the most severe mental disorders that affect people of all ages, including children and adults. The goal of this study was to look into the relationship between genetic alterations and the two diseases mentioned above as well as to develop a PPI network or related channel. The first step is to determine whether or not there is a biological relationship between them. This would assist us in connecting both of them as well as building therapeutic drugs that are effective against stress and depression disorders. Using R programs, the genes that are responsible for different diseases are acquired, pre-processed, analyzed, and mined in order to better understand them. During the study, a novel pathway was discovered. Based on common genes between the two diseases studied, the PPI network, gene-miRNA interaction, TF-gene interaction, and PDI network were established. This data can help us better understand how the PPI network binds to its ligands. We anticipate that our study will contribute to the development of new drugs for stress and depression.