1. What does ERVcancer do? 

ERVcancer is a newly developed interactive web server designed specifically for the analysis of  endogenous retrovirus (ERV) using public available RNA sequencing (RNA-seq) data. The datasets includes 151 human early embryonic samples, 8,051 human adult tissues from Genotype-Tissue Expression(GTEx) project, 932 cancer cells from cancer cell line encyclopedia (CCLE) project, as well as 6478 tumor and 634 normal tissue samples from The Cancer Genome Atlas (TCGA) project. A standardized processing pipeline was applied to analyze the RNA-seq data.  

ERVcancer provides customizable functions such as expression profiling in specific cancer cells, differential expression analysis between normal and cancer tissues, patient survival analysis, and correlation analysis between ERV subfamilies or specific ERV and genes.  

This tool was developed by Xiaoyun Lei, Song Mao from Yuan Lab, under the supervision of Prof. Kai Yuan at Xiangya Hospital, Central South University. Prof. Jinchen Li and Guihu Zhao from Xiangya Hospital also contributed valuable insights during the development of this resource.

2. How can I obtain the data and code used in ERVcancer?

All processed data can be freely retrieved from the ERVcancer database for academic use. The major code or scripts are available in http://github.com/maosong327/ERVcancer.

3. What citation should I use for ERVcancer?

Please use the following for citing ERVcancer:

Xiaoyun Lei, Song Mao, Yinshuang Li, Shi Huang, Jinchen Li, Wei Du, Chunmei Kuang, Kai Yuan. (2024). ERVcancer: a web resource designed for querying activation of human endogenous retroviruses across major cancer. Journal of Genetics and Genomics.

4. Acknowledgement

This project has been supported by the National Natural Science Foundation of China (grants 32370821, 32170821, and 92153301 to K.Y), National Key Research and Development Program of China (2021YFC2701200), Department of Science & Technology of Hunan Province (grants 2023RC1028, and 2023SK2091 to K.Y)

5. How to contact us?

If any questions about the ERVcancer, please contact:  Kai Yuan yuankai@csu.edu.cn

For more information, please visit the Yuan Lab homepage at Yuan Lab (x-mol.com)