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TIMER specifications

Information


Unique identifier OMICS_23337
Name TIMER
Alternative name Tumor IMmune Estimation Resource
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Tumor IMmune Estimation Resource

TIMER citations

 (7)
library_books

β Catenin driven adrenocortical carcinoma is characterized with immune exclusion

2018
PMCID: 5898592
PMID: 29670378
DOI: 10.2147/OTT.S159979

[…] n including age, gender, tumor stage, excessive hormone status, survival period, and follow-up time was extracted. To obtain the immunity profile of TCGA-ACC dataset, an online analytical tool named “Tumor IMmune Estimation Resource (TIMER)” was used. TIMER is a web resource for systematical evaluations of the clinical impact of different immune cells in diverse cancer types. The immune estimate o […]

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CLEC1B Expression and PD L1 Expression Predict Clinical Outcome in Hepatocellular Carcinoma with Tumor Hemorrhage12

2018
Transl Oncol
PMCID: 5884195
PMID: 29525632
DOI: 10.1016/j.tranon.2018.02.010
call_split See protocol

[…] We use Tumor Immune Estimation Resource (TIMER) web server (https://cistrome.shinyapps.io/timer/), a comprehensive analytic web tool which reanalyzed data from The Cancer Genome Atlas, to detect the CLEC1B e […]

library_books

Tumor immunity landscape in non small cell lung cancer

2018
PeerJ
PMCID: 5868477
PMID: 29593943
DOI: 10.7717/peerj.4546

[…] III having higher scores of B cells and Macrophage. Overall, the LUAD cohort showed higher infiltration than the LUSC cohort in their cytolytic-high groups. Because the cell deconvolution scores from TIMER are relative abundance, they cannot be used in our application to infer whether LUSC had a higher diversity of cell types as shown in the figures. These results suggest that CYT value is suffici […]

library_books

Global Transcriptome Analysis of RNA Abundance Regulation by ADAR in Lung Adenocarcinoma

2017
PMCID: 5828651
PMID: 29273356
DOI: 10.1016/j.ebiom.2017.12.005

[…] ignatures of apoptosis and innate immunity, we investigated the association between ADAR CN and immune infiltrates. We first downloaded tumor purity and immune infiltrate data from and then used the TIMER app (https://cistrome.shinyapps.io/timer/) (Li) to test for associations with specific immune cell types. We found that ADAR CN is significantly negatively associated with all markers of immune […]

library_books

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

2017
eLife
PMCID: 5718706
PMID: 29130882
DOI: 10.7554/eLife.26476.049

[…] g the available source code. The reference profiles available in TIMER were used directly. In addition to bulk gene expression, tumor purity estimates based on DNA copy number variation are needed in TIMER to refine the gene signature. As this information is not available in our benchmarking datasets, we kept all the original immune gene signatures for the predictions in blood. For the tumor datas […]

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Digitally deconvolving the tumor microenvironment

2016
Genome Biol
PMCID: 4993002
PMID: 27549319
DOI: 10.1186/s13059-016-1036-7
call_split See protocol

[…] n limited to microarray studies and thus are not directly applicable to TCGA.To address this issue, Liu and colleagues combined deconvolution strategies with estimations of tumor purity and presented TIMER: Tumor-IMmune Estimation Resource, a novel method for estimating the proportions of tumor–immune infiltrating subsets []. In this method, tumor purity estimations are used to find and filter gen […]

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TIMER institution(s)
Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA; Department of Statistics, Harvard University, Cambridge, MA, USA; Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA; State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
TIMER funding source(s)
Supported by NCI 1U01 CA180980, National Natural Science Foundation of China 31329003, and Chinese Scholarship council fellowship.

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