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Facilitating integrative and personalized oncology omics analysis with UCSCXenaShiny

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机构： [1]West China School of Public Health and West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, PR China. [2]School of Pharmacy, Macau University of Science and Technology, Macau, SAR, PR China. [3]Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, PR China. [4]Xiangya School of Medicine, Central South University, Changsha, 410013, PR China. [5]State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, PR China. [6]Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China. [7]Center for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau, SAR, PR China. [8]University of the Chinese Academy of Sciences, Beijing, China. [9]State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China. [10]Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA. [11]Translational Radiobiology, Department of Radiation Oncology, Universitatsklinikum Erlangen, Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany. [12]Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, PR China. [13]Thoracic Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA.

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The continuous generation of multi-omics and phenotype data is propelling advancements in precision oncology. UCSCXenaShiny was developed as an interactive tool for exploring thousands of cancer datasets available on UCSC Xena. However, its capacity for comprehensive and personalized pan-cancer data analysis is being challenged by the growing demands. Here, we introduce UCSCXenaShiny v2, a milestone update through a variety of improvements. Firstly, by integrating multidimensional data and implementing adaptable sample settings, we create a suite of robust TPC (TCGA, PCAWG, CCLE) analysis pipelines. These pipelines empower users to conduct in-depth analyses of correlation, comparison, and survival in three modes: Individual, Pan-cancer and Batch screen. Additionally, the tool includes download interfaces that enable users to access diverse data and outcomes, several features also facilitate the joint analysis of drug sensitivity and multi-omics of cancer cell lines. UCSCXenaShiny v2 is an open-source R package and a web application, freely accessible at https://github.com/openbiox/UCSCXenaShiny .© 2024. The Author(s).

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出版当年[2023]版：

大类 | 1 区

生物学

小类 | 1 区生物学

最新[2023]版：

大类 | 1 区

生物学

小类 | 1 区生物学

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第一作者机构： [1]West China School of Public Health and West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, PR China.

通讯作者：

通讯机构： [3]Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, PR China. [9]State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China. [11]Translational Radiobiology, Department of Radiation Oncology, Universitatsklinikum Erlangen, Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany. [12]Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, PR China.

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