title: TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.
abstract: The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers detailing the genomic and epigenomic alterations associated with these tumor types. Although many important discoveries have been made by TCGA's research network, opportunities still exist to implement novel methods, thereby elucidating new biological pathways and diagnostic markers. However, mining the TCGA data presents several bioinformatics challenges, such as data retrieval and integration with clinical data and other molecular data types (e.g. RNA and DNA methylation). We developed an R/Bioconductor package called TCGAbiolinks to address these challenges and offer bioinformatics solutions by using a guided workflow to allow users to query, download and perform integrative analyses of TCGA data. We combined methods from computer science and statistics into the pipeline and incorporated methodologies developed in previous TCGA marker studies and in our own group. Using four different TCGA tumor types (Kidney, Brain, Breast and Colon) as examples, we provide case studies to illustrate examples of reproducibility, integrative analysis and utilization of different Bioconductor packages to advance and accelerate novel discoveries.
authors.affiliation: Interuniversity Institute of Bioinformatics in Brussels (IB), Brussels, Belgium Machine Learning Group (MLG), Department d'Informatique, Université libre de Bruxelles (ULB), Brussels, Belgium.
authors.forename: Antonio
authors.initials: A
authors.lastname: Colaprico
authors.affiliation: Department of Genetics Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, São Paulo, Brazil.
authors.forename: Tiago C
authors.initials: TC
authors.lastname: Silva
authors.affiliation: Interuniversity Institute of Bioinformatics in Brussels (IB), Brussels, Belgium Machine Learning Group (MLG), Department d'Informatique, Université libre de Bruxelles (ULB), Brussels, Belgium.
authors.forename: Catharina
authors.initials: C
authors.lastname: Olsen
authors.affiliation: Department of Science and Technology, University of Sannio, Benevento, Italy Unlimited Software srl, Naples, Italy.
authors.forename: Luciano
authors.identifier: 0000-0001-8582-0865
authors.initials: L
authors.lastname: Garofano
authors.affiliation: Institute of Molecular Bioimaging and Physiology of the National Research Council (IBFM-CNR), Milan, Italy.
authors.forename: Claudia
authors.initials: C
authors.lastname: Cava
authors.affiliation: Physics for Complex Systems, Department of Physics, University of Turin, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Garolini
authors.affiliation: Department of Genetics Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, São Paulo, Brazil.
authors.forename: Thais S
authors.initials: TS
authors.lastname: Sabedot
authors.affiliation: Department of Genetics Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, São Paulo, Brazil.
authors.forename: Tathiane M
authors.initials: TM
authors.lastname: Malta
authors.affiliation: Department of Science and Technology, University of Sannio, Benevento, Italy Bioinformatics Laboratory, BIOGEM, Ariano Irpino, Avellino, Italy.
authors.forename: Stefano M
authors.initials: SM
authors.lastname: Pagnotta
authors.affiliation: Institute of Molecular Bioimaging and Physiology of the National Research Council (IBFM-CNR), Milan, Italy.
authors.forename: Isabella
authors.initials: I
authors.lastname: Castiglioni
authors.affiliation: Qatar Computing Research Institute (QCRI), HBKU, Doha, Qatar.
authors.forename: Michele
authors.initials: M
authors.lastname: Ceccarelli
authors.affiliation: Interuniversity Institute of Bioinformatics in Brussels (IB), Brussels, Belgium Machine Learning Group (MLG), Department d'Informatique, Université libre de Bruxelles (ULB), Brussels, Belgium gbonte@ulb.ac.be.
authors.forename: Gianluca
authors.initials: G
authors.lastname: Bontempi
authors.affiliation: Department of Genetics Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, São Paulo, Brazil houtan@usp.br.
authors.forename: Houtan
authors.initials: H
authors.lastname: Noushmehr
mesh_terms: D019313:BRCA1 Protein / Q000235:genetics; D024682:BRCA2 Protein / Q000235:genetics; D014408:Biomarkers, Tumor / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D019175:DNA Methylation / Q000235:genetics; D057225:Data Mining / Q000379:methods*; D030541:Databases, Genetic; D015894:Genome, Human / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000145:classification / Q000235:genetics*; D013223:Statistics as Topic / Q000379:methods
chemical_list: D019313:BRCA1 Protein; C492913:BRCA1 protein, human; D024682:BRCA2 Protein; C551750:BRCA2 protein, human; D014408:Biomarkers, Tumor