Akademik Veri Yönetim Sistemi
The 12th Conference of Eastern Mediterranean Region of International Biometric Society , İzmir, Türkiye, 8 - 11 Mayıs 2023, ss.57
The aim of this study is the determination of genes involved in the mechanism of intron retention in gastric cancer RNA-sequence data with the IRFinder-S algorithm. For this purpose, RNA-seq data of 11 sample tumors and normal tissue biopsies located near the tumor were examined by examining open access data from the NCBI SRA database. RNA-sequencing data from control and tumor biopsies were obtained in paired-end, fastq format. Analyzes were carried out on the virtual server of the university. As the reference genome, GRChg38-Release109 of the human genome was indexed with the STAR program. After the reference genome indexing, an index was created in IRFinder-S format. Retained introns were calculated using the BAM mode in the IRFinder-S algorithm. Statistical significance of intron retention between tumor and control groups was determined with the DESeq2 package. According to the results obtained, statistical significance was found between RNA-sequence data of gastric control and tumor tissues in terms of 91 genes (padj <0.05). In particular, the determination of intron retention at the transcriptome level of the cells and tissues of gastric cancer and other cancer types that can be examined is required. Recognition, use and validation of the algorithm and its types related to the determination of intron retention are important in the understanding and treatment of the cancer formation pathway. This study was supported by Erciyes University Scientific Research Coordination Unit with project number TYL-2022-12231.