Li 2017: TIMER, a web server for estimating immune cells in tumour genomic data
A free online tool that estimates how many of six kinds of immune cell are present in a tumour from its gene expression data, applied to more than ten thousand tumours in The Cancer Genome Atlas and used in thousands of studies since.
Overview
Li, Liu and colleagues built TIMER (Tumor IMmune Estimation Resource), a computational method and web server that infers the abundance of B cells, CD4 and CD8 T cells, neutrophils, macrophages and dendritic cells from bulk tumour RNA sequencing. They applied it to 10,897 tumours across 32 cancer types from TCGA and let users explore how immune infiltration relates to gene expression, mutations, copy number and survival. TIMER2.0 followed in 2020 with additional deconvolution methods.
- Statistical deconvolution of bulk RNA sequencing to estimate six immune cell types.
- Applied to 10,897 TCGA tumours across 32 cancer types, with a public web interface for exploring immune infiltration against genomic and clinical features.
- Updated as TIMER2.0 in 2020 with multiple deconvolution algorithms.
TIMER made immune infiltration analysis accessible to any group with tumour expression data, which is why it is cited so heavily; it is a standard first step in linking a gene or mutation to the immune state of a cancer.
- Inferred, not measured, cell abundances; different deconvolution methods can disagree.
- Bulk expression cannot resolve where immune cells sit within the tumour.
Similar pages
not linked directly; found by shared links- Key paperGalon 2006: the type, density and location of immune cells in colorectal tumours predict outcome
Shares Thorsson 2018: the immune landscape of cancer across 10,000 tumours, Immune system, Tumour-infiltrating lymphocytes (TILs).
- Key paperBinnewies 2018: understanding the tumour immune microenvironment for effective therapy
Shares Thorsson 2018: the immune landscape of cancer across 10,000 tumours, Immune system, Tumour-infiltrating lymphocytes (TILs).
- Key paperSchreiber, Old and Smyth 2011: cancer immunoediting
Shares Thorsson 2018: the immune landscape of cancer across 10,000 tumours, Immune system.
- TermT cell
Shares Immune system, Tumour-infiltrating lymphocytes (TILs).
- PathwayTumour microenvironment (TME)
Shares Immune system, Tumour-infiltrating lymphocytes (TILs), Dana-Farber Brigham Cancer Center.