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Briefings in bioinformatics
07 19, 2019;20 (4): 1524-1541.

A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data.

Zhuo Zhang, Hao Li, Shuai Jiang, Ruijiang Li, Wanying Li, Hebing Chen, Xiaochen Bo
Author Information
  1. Zhuo Zhang: Beijing Institute of Radiation Medicine, Beijing 100850, China.
  2. Hao Li: Beijing Institute of Radiation Medicine, Beijing 100850, China.
  3. Shuai Jiang: Beijing Institute of Radiation Medicine, Beijing 100850, China.
  4. Ruijiang Li: Beijing Institute of Radiation Medicine, Beijing 100850, China.
  5. Wanying Li: Beijing Institute of Radiation Medicine, Beijing 100850, China.
  6. Hebing Chen: Beijing Institute of Radiation Medicine, Beijing 100850, China.
  7. Xiaochen Bo: Beijing Institute of Radiation Medicine, Beijing 100850, China.
PMID: 29617727 DOI: 10.1093/bib/bby023

Abstract

The Cancer Genome Atlas (TCGA) is a publicly funded project that aims to catalog and discover major cancer-causing genomic alterations with the goal of creating a comprehensive 'atlas' of cancer genomic profiles. The availability of this genome-wide information provides an unprecedented opportunity to expand our knowledge of tumourigenesis. Computational analytics and mining are frequently used as effective tools for exploring this byzantine series of biological and biomedical data. However, some of the more advanced computational tools are often difficult to understand or use, thereby limiting their application by scientists who do not have a strong computational background. Hence, it is of great importance to build user-friendly interfaces that allow both computational scientists and life scientists without a computational background to gain greater biological and medical insights. To that end, this survey was designed to systematically present available Web-based tools and facilitate the use TCGA data for cancer research.

Keywords

The Cancer Genome Atlas bioinformatics tools cancer databases survey

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MeSH Term

Biomarkers, Tumor
Computational Biology
Databases, Genetic
Gene Expression Profiling
Genomics
Humans
Internet
Mutation
Neoplasms
Software
Surveys and Questionnaires
Survival Analysis
User-Computer Interface

Chemicals

Biomarkers, Tumor
Journal Article Research Support, Non-U.S. Gov't Review
Article has an altmetric score of 6

Word Cloud

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