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CTR-DB, an omnibus for patient-derived gene expression signatures correlated with cancer drug response
Zhongyang Liu1,2, Jiale Liu1, Xinyue Liu1
1State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.
Abstract:
To date, only some cancer patients can benefit from chemotherapy and targeted therapy. Drug resistance continues to be a major and challenging problem facing current cancer research. Rapidly accumulated patient-derived clinical transcriptomic data with cancer drug response bring opportunities for exploring molecular determinants of drug response, but meanwhile pose challenges for data management, integration, and reuse. Here we present the Cancer Treatment Response gene signature DataBase (CTR-DB, http://ctrdb.ncpsb.org.cn/), a unique database for basic and clinical researchers to access, integrate, and reuse clinical transcriptomes with cancer drug response. CTR-DB has collected and uniformly reprocessed 83 patient-derived pre-treatment transcriptomic source datasets with manually curated cancer drug response information, involving 28 histological cancer types, 123 drugs, and 5139 patient samples. These data are browsable, searchable, and downloadable. Moreover, CTR-DB supports single-dataset exploration (including differential gene expression, receiver operating characteristic curve, functional enrichment, sensitizing drug search, and tumor microenvironment analyses), and multiple-dataset combination and comparison, as well as biomarker validation function, which provide insights into the drug resistance mechanism, predictive biomarker discovery and validation, drug combination, and resistance mechanism heterogeneity.
Insights
A new database, CTR-DB, offers researchers access to integrated cancer drug response data. This resource aids in understanding drug resistance and discovering new biomarkers for cancer treatment.
Area of Science:
- Oncology
- Bioinformatics
- Genomics
Background:
- Chemotherapy and targeted therapies are effective for only a subset of cancer patients.
- Drug resistance remains a significant challenge in cancer research.
- Managing and integrating large-scale clinical transcriptomic data for drug response is complex.
Purpose of the Study:
- To introduce the Cancer Treatment Response gene signature DataBase (CTR-DB).
- To provide a centralized platform for accessing, integrating, and reusing clinical transcriptomic data linked to cancer drug response.
- To facilitate research into molecular determinants of drug response and resistance.
Main Methods:
- Collected and uniformly reprocessed 83 patient-derived pre-treatment transcriptomic datasets.
- Manually curated cancer drug response information for 5139 patient samples across 28 cancer types and 123 drugs.
- Developed a browsable, searchable, and downloadable database with tools for data exploration and analysis.
Main Results:
- CTR-DB integrates diverse transcriptomic data with comprehensive drug response information.
- The database supports single and multiple dataset analyses, including differential gene expression and biomarker validation.
- Facilitates exploration of drug resistance mechanisms and discovery of predictive biomarkers.
Conclusions:
- CTR-DB serves as a valuable resource for researchers studying cancer drug response and resistance.
- The database enables deeper insights into resistance mechanisms, biomarker discovery, and personalized treatment strategies.
- Facilitates the reuse of clinical transcriptomic data for advancing cancer therapy.
