Effects of Multi-Omics Characteristics on Identification of Driver Genes Using Machine Learning Algorithms. 2022

Feng Li, and Xin Chu, and Lingyun Dai, and Juan Wang, and Jinxing Liu, and Junliang Shang
School of Computer Science, Qufu Normal University, Rizhao 276826, China.

Cancer is a complex disease caused by genomic and epigenetic alterations; hence, identifying meaningful cancer drivers is an important and challenging task. Most studies have detected cancer drivers with mutated traits, while few studies consider multiple omics characteristics as important factors. In this study, we present a framework to analyze the effects of multi-omics characteristics on the identification of driver genes. We utilize four machine learning algorithms within this framework to detect cancer driver genes in pan-cancer data, including 75 characteristics among 19,636 genes. The 75 features are divided into four types and analyzed using Kullback-Leibler divergence based on CGC genes and non-CGC genes. We detect cancer driver genes in two different ways. One is to detect driver genes from a single feature type, while the other is from the top N features. The first analysis denotes that the mutational features are the best characteristics. The second analysis reveals that the top 45 features are the most effective feature combinations and superior to the mutational features. The top 45 features not only contain mutational features but also three other types of features. Therefore, our study extends the detection of cancer driver genes and provides a more comprehensive understanding of cancer mechanisms.

UI MeSH Term Description Entries
D009369 Neoplasms New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms. Benign Neoplasm,Cancer,Malignant Neoplasm,Tumor,Tumors,Benign Neoplasms,Malignancy,Malignant Neoplasms,Neoplasia,Neoplasm,Neoplasms, Benign,Cancers,Malignancies,Neoplasias,Neoplasm, Benign,Neoplasm, Malignant,Neoplasms, Malignant
D009857 Oncogenes Genes whose gain-of-function alterations lead to NEOPLASTIC CELL TRANSFORMATION. They include, for example, genes for activators or stimulators of CELL PROLIFERATION such as growth factors, growth factor receptors, protein kinases, signal transducers, nuclear phosphoproteins, and transcription factors. A prefix of "v-" before oncogene symbols indicates oncogenes captured and transmitted by RETROVIRUSES; the prefix "c-" before the gene symbol of an oncogene indicates it is the cellular homolog (PROTO-ONCOGENES) of a v-oncogene. Transforming Genes,Oncogene,Transforming Gene,Gene, Transforming,Genes, Transforming
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000069550 Machine Learning A type of ARTIFICIAL INTELLIGENCE that enable COMPUTERS to independently initiate and execute LEARNING when exposed to new data. Transfer Learning,Learning, Machine,Learning, Transfer
D000465 Algorithms A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task. Algorithm
D023281 Genomics The systematic study of the complete DNA sequences (GENOME) of organisms. Included is construction of complete genetic, physical, and transcript maps, and the analysis of this structural genomic information on a global scale such as in GENOME WIDE ASSOCIATION STUDIES. Functional Genomics,Structural Genomics,Comparative Genomics,Genomics, Comparative,Genomics, Functional,Genomics, Structural

Related Publications

Feng Li, and Xin Chu, and Lingyun Dai, and Juan Wang, and Jinxing Liu, and Junliang Shang
September 2023, Briefings in bioinformatics,
Feng Li, and Xin Chu, and Lingyun Dai, and Juan Wang, and Jinxing Liu, and Junliang Shang
November 2022, Methods (San Diego, Calif.),
Feng Li, and Xin Chu, and Lingyun Dai, and Juan Wang, and Jinxing Liu, and Junliang Shang
August 2013, Interface focus,
Feng Li, and Xin Chu, and Lingyun Dai, and Juan Wang, and Jinxing Liu, and Junliang Shang
June 2021, Scientific reports,
Feng Li, and Xin Chu, and Lingyun Dai, and Juan Wang, and Jinxing Liu, and Junliang Shang
December 2023, Heliyon,
Feng Li, and Xin Chu, and Lingyun Dai, and Juan Wang, and Jinxing Liu, and Junliang Shang
January 2015, Computers in biology and medicine,
Feng Li, and Xin Chu, and Lingyun Dai, and Juan Wang, and Jinxing Liu, and Junliang Shang
January 2022, Allergy,
Feng Li, and Xin Chu, and Lingyun Dai, and Juan Wang, and Jinxing Liu, and Junliang Shang
May 2022, International journal of molecular sciences,
Feng Li, and Xin Chu, and Lingyun Dai, and Juan Wang, and Jinxing Liu, and Junliang Shang
January 2023, Frontiers in molecular biosciences,
Feng Li, and Xin Chu, and Lingyun Dai, and Juan Wang, and Jinxing Liu, and Junliang Shang
November 2022, Briefings in bioinformatics,
Copied contents to your clipboard!