CaGe: a web-based cancer gene annotation system for cancer genomics

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Title
CaGe: a web-based cancer gene annotation system for cancer genomics
Author(s)
Young-Kyu Park; Tae-Wook Kang; Su Jin Baek; K I Kim; Seon-Young Kim; D Lee; Yong Sung Kim
Bibliographic Citation
Genomics & Informatics, vol. 10, no. 1, pp. 33-39
Publication Year
2012
Abstract
High-throughput genomic technologies (HGTs), including next-generation DNA sequencing (NGS), microarray, and serial analysis of gene expression (SAGE), have become effective experimental tools for cancer genomics to identify cancer-associated somatic genomic alterations and genes. The main hurdle in cancer genomics is to identify the real causative mutations or genes out of many candidates from an HGT-based cancer genomic analysis. One useful approach is to refer to known cancer genes and associated information. The list of known cancer genes can be used to determine candidates of cancer driver mutations, while cancer gene-related information, including gene expression, protein-protein interaction, and pathways, can be useful for scoring novel candidates. Some cancer gene or mutation databases exist for this purpose, but few specialized tools exist for an automated analysis of a long gene list from an HGT-based cancer genomic analysis. This report presents a new web-accessible bioinformatic tool, called CaGe, a cancer genome annotation system for the assessment of candidates of cancer genes from HGTbased cancer genomics. The tool provides users with and associated annotations through annotation and browsing functions. With this tool, researchers can classify their candidate genes from cancer genome studies into either previously reported or novel categories of cancer genes and gain insight into underlying carcinogenic mechanisms through a pathway analysis. We show the usefulness of CaGe by assessing its per performance in annotating somatic mutations from a published small cell lung cancer study.
Keyword
annotationcancer genehigh-throughput genomic technologymutationnext-generation sequencingpathway
ISSN
I000-0158
Publisher
South Korea
DOI
http://dx.doi.org/10.5808/GI.2012.10.1.33
Type
Article
Appears in Collections:
Korea Bioinformation Center > 1. Journal Articles
Division of Biomedical Research > Genome Editing Research Center > 1. Journal Articles
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