TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures-Reference-Cited by-同舟云学术

TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures

Published:2021-04-26 Issue:20 Volume:37 Page:3681-3683
ISSN:1367-4803
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Xie Mengyu¹,Lee Kyubum¹,Lockhart John H²,Cukras Scott D¹,Carvajal Rodrigo¹,Beg Amer A³,Flores Elsa R²,Teng Mingxiang¹^ORCID,Chung Christine H⁴,Tan Aik Choon¹^ORCID

Affiliation:

1. Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA

2. Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA

3. Department of Immunology H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA

4. Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA

Abstract

Abstract Summary The heterogeneous cell types of the tumor-immune microenvironment (TIME) play key roles in determining cancer progression, metastasis and response to treatment. We report the development of TIMEx, a novel TIME deconvolution method emphasizing on estimating infiltrating immune cells for bulk transcriptomics using pan-cancer single-cell RNA-seq signatures. We also implemented a comprehensive, user-friendly web-portal for users to evaluate TIMEx and other deconvolution methods with bulk transcriptomic profiles. Availability and implementation TIMEx web-portal is freely accessible at http://timex.moffitt.org. Supplementary information Supplementary data are available at Bioinformatics online.

Funder

Biostatistics and Bioinformatics Shared Resource at the Moffitt Cancer Center

James and Esther King Biomedical Research

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

http://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btab244/38337393/btab244.pdf

Reference15 articles.

1. xCell: digitally portraying the tissue cellular heterogeneity landscape;Aran;Genome Biol,2017

2. Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression;Becht;Genome Biol.,,2016

3. De novo transcriptome profiling of highly purified human lymphocytes primary cells;Bonnal;Sci. Data,2015

4. Quantifying tumor-infiltrating immune cells from transcriptomics data;Finotello;Cancer Immunol. Immunother,2018

5. Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data;Finotello;Gen. Med,2019

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