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Nucleic acids research
01 07, 2022;50 (D1): D1164-D1171.

CeDR Atlas: a knowledgebase of cellular drug response.

Yin-Ying Wang, Hongen Kang, Tianyi Xu, Lili Hao, Yiming Bao, Peilin Jia
Author Information
  1. Yin-Ying Wang: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  2. Hongen Kang: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  3. Tianyi Xu: China National Center for Bioinformation, Beijing 100101, China.
  4. Lili Hao: China National Center for Bioinformation, Beijing 100101, China. ORCID
  5. Yiming Bao: China National Center for Bioinformation, Beijing 100101, China.
  6. Peilin Jia: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. ORCID
PMID: 34634794 DOI: 10.1093/nar/gkab897

Abstract

Drug response to many diseases varies dramatically due to the complex genomics and functional features and contexts. Cellular diversity of human tissues, especially tumors, is one of the major contributing factors to the different drug response in different samples. With the accumulation of single-cell RNA sequencing (scRNA-seq) data, it is now possible to study the drug response to different treatments at the single cell resolution. Here, we present CeDR Atlas (available at https://ngdc.cncb.ac.cn/cedr), a knowledgebase reporting computational inference of cellular drug response for hundreds of cell types from various tissues. We took advantage of the high-throughput profiling of drug-induced gene expression available through the Connectivity Map resource (CMap) as well as hundreds of scRNA-seq data covering cells from a wide variety of organs/tissues, diseases, and conditions. Currently, CeDR maintains the results for more than 582 single cell data objects for human, mouse and cell lines, including about 140 phenotypes and 1250 tissue-cell combination types. All the results can be explored and searched by keywords for drugs, cell types, tissues, diseases, and signature genes. Overall, CeDR fine maps drug response at cellular resolution and sheds lights on the design of combinatorial treatments, drug resistance and even drug side effects.

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MeSH Term

Animals
Biomarkers, Pharmacological
Databases, Factual
Gene Expression Profiling
Humans
Knowledge Bases
Mice
Neoplasms
RNA-Seq
Single-Cell Analysis
Software
Exome Sequencing

Chemicals

Biomarkers, Pharmacological
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

Database Commons: DBC007424 (CeDR)

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