Oncotarget

Reviews:

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

Katarzyna Klonowska, Karol Czubak, Marzena Wojciechowska, Luiza Handschuh, Agnieszka Zmienko, Marek Figlerowicz, Hanna Dams-Kozlowska and Piotr Kozlowski _

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Oncotarget. 2016; 7:176-192. https://doi.org/10.18632/oncotarget.6128

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Abstract

Katarzyna Klonowska1, Karol Czubak1, Marzena Wojciechowska1, Luiza Handschuh1,2, Agnieszka Zmienko1,3, Marek Figlerowicz1,3, Hanna Dams-Kozlowska4,5 and Piotr Kozlowski1

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.


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