# Li 2020: TIMER2.0 for analysis of tumour-infiltrating immune cells

Source: https://onco.cc/key-papers/paper-li-timer2-nar-2020/  
OnCo record `paper-li-timer2-nar-2020` (Key paper). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

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.

## Summary

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.

## Fields

- Kind: Key paper
- Last checked: 2026-09-08
- Journal: Nucleic Acids Research
- Year: 2020
- DOI: 10.1093/nar/gkaa407
- Authors: Li T, Fu J, Zeng Z, et al.
- Findings: 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.
- What it means: 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.
- Caveats: Estimates are inferred from bulk expression and vary by algorithm.; Cannot resolve spatial location of immune cells.

## Sources

- Full text (DOI): https://doi.org/10.1093/nar/gkaa407
- TIMER2.0: http://timer.cistrome.org/

## Connected records

- key papers: [Li 2017: TIMER, a web server for estimating immune cells in tumour genomic data](https://onco.cc/key-papers/paper-li-timer-tumour-infiltrating-immune-cells-cancerres-2017/)
- collections: [TCGA / NCI Genomic Data Commons](https://onco.cc/collections/tcga-gdc/)
- institutions: [Dana-Farber Brigham Cancer Center](https://onco.cc/institutions/dana-farber/)
- terms: [Immune system](https://onco.cc/terms/immune-system/), [Tumour-infiltrating lymphocytes (TILs)](https://onco.cc/terms/tils/)

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