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

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

doi:10.1093/bioinformatics/btab244

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

Bioinformatics. 2021 Oct 25;37(20):3681-3683. doi: 10.1093/bioinformatics/btab244.

Authors

Affiliations

¹ Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
² Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
³ Department of Immunology H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
⁴ Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.

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.

Abstract

Grants and funding