Genetic Analysis of Prostate Cancer with Computer Science Methods

March 28, 2023 · Entered Twilight · 🏛 arXiv.org

Repo contents: .ipynb_checkpoints, BOSAM_implementation.ipynb, Gene_Network.ipynb, ML_predicton.ipynb, Master_Report.pdf, Untitled.ipynb, cancer_data, cancer_project.ipynb, gene_network_analysis.ipynb, img, mRNA_analysis.ipynb, network&XGBoost.ipynb, preparation.py, project_report.tex

Authors Yuxuan Li, Shi Zhou arXiv ID 2303.15851 Category cs.IR: Information Retrieval Cross-listed q-bio.QM Citations 0 Venue arXiv.org Repository https://github.com/zcablii/Master_cancer_project ⭐ 1 Last Checked 3 months ago

Abstract

Metastatic prostate cancer is one of the most common cancers in men. In the advanced stages of prostate cancer, tumours can metastasise to other tissues in the body, which is fatal. In this thesis, we performed a genetic analysis of prostate cancer tumours at different metastatic sites using data science, machine learning and topological network analysis methods. We presented a general procedure for pre-processing gene expression datasets and pre-filtering significant genes by analytical methods. We then used machine learning models for further key gene filtering and secondary site tumour classification. Finally, we performed gene co-expression network analysis and community detection on samples from different prostate cancer secondary site types. In this work, 13 of the 14,379 genes were selected as the most metastatic prostate cancer related genes, achieving approximately 92% accuracy under cross-validation. In addition, we provide preliminary insights into the co-expression patterns of genes in gene co-expression networks. Project code is available at https://github.com/zcablii/Master_cancer_project.