S-score: a scoring system for the identification and prioritization of predicted cancer genes.
A new method, which allows for the identification and prioritization of predicted cancer genes for future analysis, is presented. This method generates a gene-specific score called the "S-Score" by incorporating data from different types of analysis including mutation screening, methylation status, copy-number variation and expression profiling. The method was applied to the data from The Cancer Genome Atlas and allowed the identification of known and potentially new oncogenes and tumor suppressors associated with different clinical features including shortest term of survival in ovarian cancer patients and hormonal subtypes in breast cancer patients. Furthermore, for the first time a genome-wide search for genes that behave as oncogenes and tumor suppressors in different tumor types was performed. We envisage that the S-score can be used as a standard method for the identification and prioritization of cancer genes for follow-up studies.
Institute of Bioinformatics and Biotechnology, São Paulo, Brazil; Center for Cell Therapy and Regional Blood Center, Department of Clinical Medicine, Faculty of Medicine, University of São Paulo, Ribeirão Preto, Brazil; International Research Center, CIPE/AC Camargo Cancer Center, São Paulo, Brazil.
Jorge E S
JE
de Souza
Institute of Bioinformatics and Biotechnology, São Paulo, Brazil; Brain Institute, UFRN, Natal, Brazil.
André F
AF
Fonseca
Institute of Bioinformatics and Biotechnology, São Paulo, Brazil; International Research Center, CIPE/AC Camargo Cancer Center, São Paulo, Brazil.
Renan
R
Valieris
International Research Center, CIPE/AC Camargo Cancer Center, São Paulo, Brazil.
Dirce M
DM
Carraro
Moores-UCSD Cancer Center and Department of Medicine, University of California San Diego School of Medicine, San Diego, California, United States of America.
Jean Y J
JY
Wang
Moores-UCSD Cancer Center and Department of Medicine, University of California San Diego School of Medicine, San Diego, California, United States of America; Ludwig Institute for Cancer Research, San Diego Branch, Department of Medicine and Cellular and Molecular Medicine, Moores-UCSD Cancer Center and Institute of Genomic Medicine, University of California San Diego School of Medicine, San Diego, California, United States of America.
Richard D
RD
Kolodner
Brain Institute, UFRN, Natal, Brazil.
Sandro J
SJ
de Souza
D019295:Computational Biology / Q000379:methods*; D056915:DNA Copy Number Variations / Q000235:genetics; D005260:Female; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D052138:Genes, Neoplasm / Q000235:genetics*; D023281:Genomics; D006801:Humans; D008745:Methylation; D009154:Mutation / Q000235:genetics; D009369:Neoplasms / Q000235:genetics*; D009857:Oncogenes / Q000235:genetics