title: RWCFusion: identifying phenotype-specific cancer driver gene fusions based on fusion pair random walk scoring method.
abstract: While gene fusions have been increasingly detected by next-generation sequencing (NGS) technologies based methods in human cancers, these methods have limitations in identifying driver fusions. In addition, the existing methods to identify driver gene fusions ignored the specificity among different cancers or only considered their local rather than global topology features in networks. Here, we proposed a novel network-based method, called RWCFusion, to identify phenotype-specific cancer driver gene fusions. To evaluate its performance, we used leave-one-out cross-validation in 35 cancers and achieved a high AUC value 0.925 for overall cancers and an average 0.929 for signal cancer. Furthermore, we classified 35 cancers into two classes: haematological and solid, of which the haematological got a highly AUC which is up to 0.968. Finally, we applied RWCFusion to breast cancer and found that top 13 gene fusions, such as BCAS3-BCAS4, NOTCH-NUP214, MED13-BCAS3 and CARM-SMARCA4, have been previously proved to be drivers for breast cancer. Additionally, 8 among the top 10 of the remaining candidate gene fusions, such as SULF2-ZNF217, MED1-ACSF2, and ACACA-STAC2, were inferred to be potential driver gene fusions of breast cancer by us.
authors: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China.|The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China.
authors: Jianmei
authors: J
authors: Zhao
authors: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China.
authors: Xuecang
authors: X
authors: Li
authors: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors: Qianlan
authors: Q
authors: Yao
authors: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China.
authors: Meng
authors: M
authors: Li
authors: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China.
authors: Jian
authors: J
authors: Zhang
authors: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China.
authors: Bo
authors: B
authors: Ai
authors: Department of Mathematics, Heilongjiang Institute of Technology, Harbin, 150050, China.
authors: Wei
authors: W
authors: Liu
authors: School of Nursing and Pharmacology, Daqing Campus, Harbin Medical University, Daqing, 163319, China.
authors: Qiuyu
authors: Q
authors: Wang
authors: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China.
authors: Chenchen
authors: C
authors: Feng
authors: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China.
authors: Yuejuan
authors: Y
authors: Liu
authors: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China.
authors: Xuefeng
authors: X
authors: Bai
authors: School of Nursing and Pharmacology, Daqing Campus, Harbin Medical University, Daqing, 163319, China.
authors: Chao
authors: C
authors: Song
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors: Shang
authors: S
authors: Li
authors: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China.
authors: Enmin
authors: E
authors: Li
authors: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China.
authors: Liyan
authors: L
authors: Xu
authors: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China.|The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China.
authors: Chunquan
authors: C
authors: Li
mesh_terms: D019540:Area Under Curve; D001943:Breast Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D050939:Gene Fusion; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D015514:Oncogene Proteins, Fusion / Q000235:genetics; D010641:Phenotype; D025941:Protein Interaction Mapping; D017423:Sequence Analysis, RNA
chemical_list: D015514:Oncogene Proteins, Fusion
keywords: cancer; driver; gene fusion; network