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TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures

2021; Oxford University Press; Volume: 37; Issue: 20 Linguagem: Inglês

10.1093/bioinformatics/btab244

1367-4811

Mengyu Xie, Kyubum Lee, John H. Lockhart, Scott D Cukras, Rodrigo Carvajal, Amer A. Beg, Elsa R. Flores, Mingxiang Teng, Christine H. Chung, Aik Choon Tan,

Cancer-related molecular mechanisms research

Abstract Summary The heterogeneous cell types of the tumor-immune microenvironment (TIME) play key roles in determining cancer progression, metastasis and response to treatment. We report the development of TIMEx, a novel TIME deconvolution method emphasizing on estimating infiltrating immune cells for bulk transcriptomics using pan-cancer single-cell RNA-seq signatures. We also implemented a comprehensive, user-friendly web-portal for users to evaluate TIMEx and other deconvolution methods with bulk transcriptomic profiles. Availability and implementation TIMEx web-portal is freely accessible at http://timex.moffitt.org. Supplementary information Supplementary data are available at Bioinformatics online.