TIMEDB: tumor immune micro-environment cell composition database with automatic analysis and interactive visualization

Author:

Wang Xueying12ORCID,Chen Lingxi12ORCID,Liu Wei1,Zhang Yuanzheng3,Liu Dawei4,Zhou Chenxin5,Shi Shuai6,Dong Jiajie1,Lai Zhengtao5,Zhao Bingran5,Zhang Wenjingyu5,Cheng Haoyue7,Li Shuaicheng12ORCID

Affiliation:

1. Department of Computer Science, City University of Hong Kong , Hong Kong, China

2. City University of Hong Kong Shenzhen Research Institute , Guangdong, China

3. School of Medicine and Biological Information Engineering, Northeastern University , Shenyang, Liaoning, China

4. School of Software, Northeastern University , Shenyang, Liaoning, China

5. School of Business Administration, Northeastern University , Shenyang, Liaoning, China

6. School of Creative Media, City University of Hong Kong , Hong Kong, China

7. Department of Clinical Pathology, Capital Medical University , Beijing, China

Abstract

Abstract Deciphering the cell-type composition in the tumor immune microenvironment (TIME) can significantly increase the efficacy of cancer treatment and improve the prognosis of cancer. Such a task has benefited from microarrays and RNA sequencing technologies, which have been widely adopted in cancer studies, resulting in extensive expression profiles with clinical phenotypes across multiple cancers. Current state-of-the-art tools can infer cell-type composition from bulk expression profiles, providing the possibility of investigating the inter-heterogeneity and intra-heterogeneity of TIME across cancer types. Much can be gained from these tools in conjunction with a well-curated database of TIME cell-type composition data, accompanied by the corresponding clinical information. However, currently available databases fall short in data volume, multi-platform dataset integration, and tool integration. In this work, we introduce TIMEDB (https://timedb.deepomics.org), an online database for human tumor immune microenvironment cell-type composition estimated from bulk expression profiles. TIMEDB stores manually curated expression profiles, cell-type composition profiles, and the corresponding clinical information of a total of 39,706 samples from 546 datasets across 43 cancer types. TIMEDB comes readily equipped with online tools for automatic analysis and interactive visualization, and aims to serve the community as a convenient tool for investigating the human tumor microenvironment.

Funder

CityU/UGC Research Matching Grant Scheme

SIRG

The Science Technology and Innovation Committee of Shenzhen Municipality

Publisher

Oxford University Press (OUP)

Subject

Genetics

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