Li 2020: TIMER2.0 for analysis of tumour-infiltrating immune cells
The updated version of the TIMER web tool, which estimates immune cell content in tumour gene expression data using six different algorithms side by side so users can see where they agree.
Overview
Li, Liu and colleagues released TIMER2.0, extending their immune estimation web server with multiple deconvolution methods, including TIMER, CIBERSORT, quanTIseq, xCell, MCP-counter and EPIC, applied to TCGA tumours and to user-uploaded expression data. The server lets users relate immune infiltration estimates to gene expression, somatic mutations, copy number and survival across cancer types, and to compare the estimates from different algorithms, which often disagree.
- Six immune deconvolution algorithms available side by side on one web server.
- Modules link immune estimates to gene expression, mutation, copy number and outcome across TCGA cancer types.
- Accepts user-uploaded expression profiles for estimation.
TIMER2.0 is one of the most used tools in cancer immunogenomics and its multi-algorithm design is a reminder that computational immune cell estimates are model-dependent and should be cross-checked.
- Estimates are inferred from bulk expression and vary by algorithm.
- Cannot resolve spatial location of immune cells.
Similar pages
not linked directly; found by shared links- Key paperThorsson 2018: the immune landscape of cancer across 10,000 tumours
Shares Li 2017: TIMER, a web server for estimating immune cells in tumour genomic data, Immune system, Tumour-infiltrating lymphocytes (TILs).
- Key paperGalon 2006: the type, density and location of immune cells in colorectal tumours predict outcome
Shares Immune system, Tumour-infiltrating lymphocytes (TILs).
- Key paperBinnewies 2018: understanding the tumour immune microenvironment for effective therapy
Shares Immune system, Tumour-infiltrating lymphocytes (TILs).
- TermT cell
Shares Immune system, Tumour-infiltrating lymphocytes (TILs).
- PathwayTumour microenvironment (TME)
Shares Immune system, Tumour-infiltrating lymphocytes (TILs), Dana-Farber Brigham Cancer Center.