Oncogenomic portals for the visualization and analysis of genome-wide cancer data.
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.
European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
Katarzyna
K
Klonowska
European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
Karol
K
Czubak
European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
Marzena
M
Wojciechowska
European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.|Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland.
Luiza
L
Handschuh
European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.|Institute of Computing Sciences, Poznan University of Technology, Poznan, Poland.
Agnieszka
A
Zmienko
European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.|Institute of Computing Sciences, Poznan University of Technology, Poznan, Poland.
Marek
M
Figlerowicz
Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland.|Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.
Hanna
H
Dams-Kozlowska
European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
Piotr
P
Kozlowski
D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data; D056915:DNA Copy Number Variations; D057225:Data Mining / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D055106:Genome-Wide Association Study / Q000379:methods* / Q000706:statistics & numerical data; D023281:Genomics / Q000379:methods* / Q000706:statistics & numerical data; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D015203:Reproducibility of Results
COSMIC; IntOGen; PPISURV/MIRUMIR; Tumorscape; cBioPortal