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GSCA: an integrated platform for gene set cancer analysis at genomic, pharmacogenomic and immunogenomic levels.
Liu, Chun-Jie; Hu, Fei-Fei; Xie, Gui-Yan; Miao, Ya-Ru; Li, Xin-Wen; Zeng, Yan; Guo, An-Yuan.
Afiliación
  • Liu CJ; Wuhan University of Science and Technology and Huazhong University of Science and Technology.
  • Hu FF; Wuhan University of Science and Technology.
  • Xie GY; Huazhong University of Science and Technology.
  • Miao YR; Huazhong University of Science and Technology.
  • Li XW; Wuhan University of Science and Technology.
  • Zeng Y; Wuhan University of Science and Technology.
  • Guo AY; Huazhong University of Science and Technology.
Brief Bioinform ; 24(1)2023 01 19.
Article en En | MEDLINE | ID: mdl-36549921
Cancer initiation and progression are likely caused by the dysregulation of biological pathways. Gene set analysis (GSA) could improve the signal-to-noise ratio and identify potential biological insights on the gene set level. However, platforms exploring cancer multi-omics data using GSA methods are lacking. In this study, we upgraded our GSCALite to GSCA (gene set cancer analysis, http://bioinfo.life.hust.edu.cn/GSCA) for cancer GSA at genomic, pharmacogenomic and immunogenomic levels. In this improved GSCA, we integrated expression, mutation, drug sensitivity and clinical data from four public data sources for 33 cancer types. We introduced useful features to GSCA, including associations between immune infiltration with gene expression and genomic variations, and associations between gene set expression/mutation and clinical outcomes. GSCA has four main functional modules for cancer GSA to explore, analyze and visualize expression, genomic variations, tumor immune infiltration, drug sensitivity and their associations with clinical outcomes. We used case studies of three gene sets: (i) seven cell cycle genes, (ii) tumor suppressor genes of PI3K pathway and (iii) oncogenes of PI3K pathway to prove the advantage of GSCA over single gene analysis. We found novel associations of gene set expression and mutation with clinical outcomes in different cancer types on gene set level, while on single gene analysis level, they are not significant associations. In conclusion, GSCA is a user-friendly web server and a useful resource for conducting hypothesis tests by using GSA methods at genomic, pharmacogenomic and immunogenomic levels.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Farmacogenética / Neoplasias Límite: Humans Idioma: En Revista: Brief Bioinform Asunto de la revista: BIOLOGIA / INFORMATICA MEDICA Año: 2023 Tipo del documento: Article Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Farmacogenética / Neoplasias Límite: Humans Idioma: En Revista: Brief Bioinform Asunto de la revista: BIOLOGIA / INFORMATICA MEDICA Año: 2023 Tipo del documento: Article Pais de publicación: Reino Unido