Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration
Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration
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Cold Spring Harbor: Cold Spring Harbor Laboratory Press
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Language
English
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Cold Spring Harbor: Cold Spring Harbor Laboratory Press
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Transcriptomic deconvolution in cancer and other heterogeneous tissues remains challenging. Available methods lack the ability to estimate both component-specific proportions and expression profiles for individual samples. We present DeMixT, a new tool to deconvolve high dimensional data from mixtures of more than two components. DeMixT implements an iterated conditional mode algorithm and a novel gene-set-based component merging approach to improve accuracy. In a series of experimental validation studies and application to TCGA data, DeMixT showed high accuracy. Improved deconvolution is an important step towards linking tumor transcriptomic data with clinical outcomes. An R package, scripts and data are available: https://github.com/wwylab/DeMixT/....
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Full title
Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration
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TN_cdi_proquest_journals_2071253326
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https://devfeature-collection.sl.nsw.gov.au/record/TN_cdi_proquest_journals_2071253326
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E-ISSN
2692-8205
DOI
10.1101/146795
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https://www.proquest.com/docview/2071253326?pq-origsite=primo&accountid=13902
