{"entity":{"id":"paper-li-timer-tumour-infiltrating-immune-cells-cancerres-2017","kind":"paper","name":"Li 2017: TIMER, a web server for estimating immune cells in tumour genomic data","aka":[],"tldr":"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.","summary":"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.","asOf":"2026-09-08","links":[{"label":"Full text (DOI)","url":"https://doi.org/10.1158/0008-5472.CAN-17-0307"},{"label":"TIMER2.0","url":"http://timer.cistrome.org/"}],"tags":[],"related":["tcga-gdc","paper-thorsson-immune-landscape-of-cancer-immunity-2018"],"cancers":[],"sections":[],"technologies":[],"targets":[],"drugs":[],"companies":[],"institutions":["dana-farber"],"pathways":[],"terms":["tils","immune-system"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"notes":[],"journal":"Cancer Research","year":2017,"doi":"10.1158/0008-5472.CAN-17-0307","authors":"Li T, Fan J, Wang B, et al.","paperType":"methods","findings":["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."],"whatItMeans":"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.","caveats":["Inferred, not measured, cell abundances; different deconvolution methods can disagree.","Bulk expression cannot resolve where immune cells sit within the tumour."],"changedPractice":false},"route":"/key-papers/paper-li-timer-tumour-infiltrating-immune-cells-cancerres-2017/","neighbours":{"collection":[{"id":"tcga-gdc","kind":"collection","name":"TCGA / NCI Genomic Data Commons","route":"/collections/tcga-gdc/"}],"paper":[{"id":"paper-li-timer2-nar-2020","kind":"paper","name":"Li 2020: TIMER2.0 for analysis of tumour-infiltrating immune cells","route":"/key-papers/paper-li-timer2-nar-2020/"},{"id":"paper-thorsson-immune-landscape-of-cancer-immunity-2018","kind":"paper","name":"Thorsson 2018: the immune landscape of cancer across 10,000 tumours","route":"/key-papers/paper-thorsson-immune-landscape-of-cancer-immunity-2018/"}],"institution":[{"id":"dana-farber","kind":"institution","name":"Dana-Farber Brigham Cancer Center","route":"/institutions/dana-farber/"}],"term":[{"id":"immune-system","kind":"term","name":"Immune system","route":"/terms/immune-system/"},{"id":"tils","kind":"term","name":"Tumour-infiltrating lymphocytes (TILs)","route":"/terms/tils/"}]}}