Computational methods for cancer driver discovery: A survey. 2021

Vu Viet Hoang Pham, and Lin Liu, and Cameron Bracken, and Gregory Goodall, and Jiuyong Li, and Thuc Duy Le
UniSA STEM, University of South Australia, Mawson Lakes, SA 5095, AU.

Identifying the genes responsible for driving cancer is of critical importance for directing treatment. Accordingly, multiple computational tools have been developed to facilitate this task. Due to the different methods employed by these tools, different data considered by the tools, and the rapidly evolving nature of the field, the selection of an appropriate tool for cancer driver discovery is not straightforward. This survey seeks to provide a comprehensive review of the different computational methods for discovering cancer drivers. We categorise the methods into three groups; methods for single driver identification, methods for driver module identification, and methods for identifying personalised cancer drivers. In addition to providing a "one-stop" reference of these methods, by evaluating and comparing their performance, we also provide readers the information about the different capabilities of the methods in identifying biologically significant cancer drivers. The biologically relevant information identified by these tools can be seen through the enrichment of discovered cancer drivers in GO biological processes and KEGG pathways and through our identification of a small cancer-driver cohort that is capable of stratifying patient survival.

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
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D015398 Signal Transduction The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway. Cell Signaling,Receptor-Mediated Signal Transduction,Signal Pathways,Receptor Mediated Signal Transduction,Signal Transduction Pathways,Signal Transduction Systems,Pathway, Signal,Pathway, Signal Transduction,Pathways, Signal,Pathways, Signal Transduction,Receptor-Mediated Signal Transductions,Signal Pathway,Signal Transduction Pathway,Signal Transduction System,Signal Transduction, Receptor-Mediated,Signal Transductions,Signal Transductions, Receptor-Mediated,System, Signal Transduction,Systems, Signal Transduction,Transduction, Signal,Transductions, Signal
D019295 Computational Biology A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets. Bioinformatics,Molecular Biology, Computational,Bio-Informatics,Biology, Computational,Computational Molecular Biology,Bio Informatics,Bio-Informatic,Bioinformatic,Biologies, Computational Molecular,Biology, Computational Molecular,Computational Molecular Biologies,Molecular Biologies, Computational

Related Publications

Vu Viet Hoang Pham, and Lin Liu, and Cameron Bracken, and Gregory Goodall, and Jiuyong Li, and Thuc Duy Le
December 2023, Mathematical biosciences and engineering : MBE,
Vu Viet Hoang Pham, and Lin Liu, and Cameron Bracken, and Gregory Goodall, and Jiuyong Li, and Thuc Duy Le
March 2022, Briefings in bioinformatics,
Vu Viet Hoang Pham, and Lin Liu, and Cameron Bracken, and Gregory Goodall, and Jiuyong Li, and Thuc Duy Le
May 2022, Briefings in bioinformatics,
Vu Viet Hoang Pham, and Lin Liu, and Cameron Bracken, and Gregory Goodall, and Jiuyong Li, and Thuc Duy Le
January 2015, BMC genomics,
Vu Viet Hoang Pham, and Lin Liu, and Cameron Bracken, and Gregory Goodall, and Jiuyong Li, and Thuc Duy Le
January 2016, Journal of medicinal chemistry,
Vu Viet Hoang Pham, and Lin Liu, and Cameron Bracken, and Gregory Goodall, and Jiuyong Li, and Thuc Duy Le
January 2016, Beilstein journal of organic chemistry,
Vu Viet Hoang Pham, and Lin Liu, and Cameron Bracken, and Gregory Goodall, and Jiuyong Li, and Thuc Duy Le
January 2014, Pharmacological reviews,
Vu Viet Hoang Pham, and Lin Liu, and Cameron Bracken, and Gregory Goodall, and Jiuyong Li, and Thuc Duy Le
January 2016, IEEE/ACM transactions on computational biology and bioinformatics,
Vu Viet Hoang Pham, and Lin Liu, and Cameron Bracken, and Gregory Goodall, and Jiuyong Li, and Thuc Duy Le
December 2007, Computer methods and programs in biomedicine,
Vu Viet Hoang Pham, and Lin Liu, and Cameron Bracken, and Gregory Goodall, and Jiuyong Li, and Thuc Duy Le
June 2023, Journal of molecular graphics & modelling,
Copied contents to your clipboard!