Oncogenomic portals for the visualization and analysis of genome-wide cancer data

// Katarzyna Klonowska 1 , Karol Czubak 1 , Marzena Wojciechowska 1 , Luiza Handschuh 1,2 , Agnieszka Zmienko 1,3 , Marek Figlerowicz 1,3 , Hanna Dams-Kozlowska 4,5 and Piotr Kozlowski 1 1 European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland 2 Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland 3 Institute of Computing Sciences, Poznan University of Technology, Poznan, Poland 4 Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland 5 Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland Correspondence to: Piotr Kozlowski, email: // Keywords : cBioPortal, COSMIC, IntOGen, PPISURV/MIRUMIR, Tumorscape Received : June 18, 2015 Accepted : September 28, 2015 Published : October 15, 2015 Abstract Somatically acquired genomic alterations that drive oncogenic cellular processes are of great scientific and clinical interest. Since the initiation of large-scale cancer genomic projects (e.g., the Cancer Genome Project, The Cancer Genome Atlas, and the International Cancer Genome Consortium cancer genome projects), a number of web-based portals have been created to facilitate access to multidimensional oncogenomic data and assist with the interpretation of the data. The portals provide the visualization of small-size mutations, copy number variations, methylation, and gene/protein expression data that can be correlated with the available clinical, epidemiological, and molecular features. Additionally, the portals enable to analyze the gathered data with the use of various user-friendly statistical tools. Herein, we present a highly illustrated review of seven portals, i.e., Tumorscape, UCSC Cancer Genomics Browser, ICGC Data Portal, COSMIC, cBioPortal, IntOGen, and BioProfiling.de. All of the selected portals are user-friendly and can be exploited by scientists from different cancer-associated fields, including those without bioinformatics background. It is expected that the use of the portals will contribute to a better understanding of cancer molecular etiology and will ultimately accelerate the translation of genomic knowledge into clinical practice.