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Bioinformatics tools and resources for cancer and application
Jin Huang1, Lingzi Mao2, Qian Lei1
1Department of Thoracic Surgery, West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
Chinese Medical Journal
|July 30, 2024
Summary
This review summarizes bioinformatics tools for analyzing cancer omics data. It aids researchers in selecting resources for multi-omics, regulatory, treatment, immune, and single-cell analyses in cancer research.
Area of Science:
- Bioinformatics
- Cancer Research
- Computational Biology
Background:
- High-throughput technologies have generated vast amounts of cancer omics data.
- Effective utilization and sharing of this data are critical for advancing cancer research and precision medicine.
- Traditional cancer research focused on fundamental pathways and genes, but the omics era demands new analytical approaches.
Purpose of the Study:
- To review and summarize publicly available bioinformatics tools and resources for pan-cancer multi-omics analysis.
- To provide researchers with a guide for selecting appropriate tools for various cancer research areas, including regulatory analysis, treatment and prognosis, immune infiltration, immune repertoire, driver gene/mutation analysis, and single-cell analysis.
- To facilitate the efficient use and sharing of large-scale cancer omics data.
Main Methods:
- Systematic review of publicly available bioinformatics tools and databases.
- Categorization of tools based on their application in cancer research (e.g., multi-omics, immune analysis, single-cell).
- Description of the functions and utility of summarized resources for cancer researchers.
Main Results:
- A comprehensive summary of diverse bioinformatics tools and resources relevant to cancer research is presented.
- Tools are organized by key areas of cancer multi-omics analysis, tumorigenesis regulation, treatment/prognosis, immune analysis, and single-cell studies.
- The review highlights the growing landscape of computational resources available for cancer data analysis.
Conclusions:
- Bioinformatics tools are essential for navigating and interpreting large-scale cancer omics data.
- This review serves as a valuable resource for researchers seeking to identify suitable computational tools for their specific cancer research needs.
- Effective use of these tools will accelerate discoveries in cancer research and the development of precision medicine.
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