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.
Highlights
Cancer encompasses a broad spectrum of diseases (>100) that arise from somatically acquired genetic, epigenetic, transcriptomic, and proteomic alterations that have accumulated in the genomes of cancer cells [1]
Among other noteworthy portals that provide sets of visualization tools that are helpful for oncogenomic data analysis are Oasis [100, 101], Oncomine [102, 103], Cancer Genetics Web [104], and CaSNP [105, 106]
The Cancer Genetics Web is a web-based tool that can be used to gather literature that is related to a specific cancer type/predisposing syndrome or a gene of interest that is potentially associated with cancer
Summary
Cancer encompasses a broad spectrum of diseases (>100) that arise from somatically acquired genetic, epigenetic, transcriptomic, and proteomic alterations that have accumulated in the genomes of cancer cells [1]. There is the possibility of viewing PARADIGM datasets to gather a sample-specific “gene activity level.” This parameter (obtained using the PARADIGM method) [20] provides the incorporation of pathway interactions (which are deposited in the NCI Pathway Interaction Database) [21] and the integration of data with regard to different types of oncogenomic alterations, e.g., changes in the expression or copy number of a given gene [16].
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