CaGe: A Web-Based Cancer Gene Annotation System for Cancer Genomics
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...
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| Format: | Article |
| Language: | English |
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BioMed Central
2012-03-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-10-33.pdf |
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| author | Young-Kyu Park Tae-Wook Kang Su-Jin Baek Kwon-Il Kim Seon-Young Kim Doheon Lee Yong Sung Kim |
| author_facet | Young-Kyu Park Tae-Wook Kang Su-Jin Baek Kwon-Il Kim Seon-Young Kim Doheon Lee Yong Sung Kim |
| author_sort | Young-Kyu Park |
| collection | DOAJ |
| description | 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 HGT-based cancer genomics. The tool provides users with information on cancer-related genes, mutations, pathways, 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 performance in annotating somatic mutations from a published small cell lung cancer study. |
| format | Article |
| id | doaj-art-edb0c5f1d55f42879c5a800c6d193ae3 |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2012-03-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-edb0c5f1d55f42879c5a800c6d193ae32025-02-02T21:22:21ZengBioMed CentralGenomics & Informatics1598-866X2234-07422012-03-01101333910.5808/GI.2012.10.1.3329CaGe: A Web-Based Cancer Gene Annotation System for Cancer GenomicsYoung-Kyu Park0Tae-Wook Kang1Su-Jin Baek2Kwon-Il Kim3Seon-Young Kim4Doheon Lee5Yong Sung Kim6Medical Genomics Research Center, KRIBB, Daejeon 305-806, Korea.Medical Genomics Research Center, KRIBB, Daejeon 305-806, Korea.Medical Genomics Research Center, KRIBB, Daejeon 305-806, Korea.Department of Bio and Brain Engineering, KAIST, Daejeon 305-701, Korea.Medical Genomics Research Center, KRIBB, Daejeon 305-806, Korea.Department of Bio and Brain Engineering, KAIST, Daejeon 305-701, Korea.Medical Genomics Research Center, KRIBB, Daejeon 305-806, Korea.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 HGT-based cancer genomics. The tool provides users with information on cancer-related genes, mutations, pathways, 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 performance in annotating somatic mutations from a published small cell lung cancer study.http://genominfo.org/upload/pdf/gni-10-33.pdfannotationcancer genehigh-throughput genomic technologymutationnext-generation sequencingpathway |
| spellingShingle | Young-Kyu Park Tae-Wook Kang Su-Jin Baek Kwon-Il Kim Seon-Young Kim Doheon Lee Yong Sung Kim CaGe: A Web-Based Cancer Gene Annotation System for Cancer Genomics Genomics & Informatics annotation cancer gene high-throughput genomic technology mutation next-generation sequencing pathway |
| title | CaGe: A Web-Based Cancer Gene Annotation System for Cancer Genomics |
| title_full | CaGe: A Web-Based Cancer Gene Annotation System for Cancer Genomics |
| title_fullStr | CaGe: A Web-Based Cancer Gene Annotation System for Cancer Genomics |
| title_full_unstemmed | CaGe: A Web-Based Cancer Gene Annotation System for Cancer Genomics |
| title_short | CaGe: A Web-Based Cancer Gene Annotation System for Cancer Genomics |
| title_sort | cage a web based cancer gene annotation system for cancer genomics |
| topic | annotation cancer gene high-throughput genomic technology mutation next-generation sequencing pathway |
| url | http://genominfo.org/upload/pdf/gni-10-33.pdf |
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