Abstract
Tissues are a complex milieu of cell types of different lineages and subtypes, each with its own unique transcriptomic profile. Bulk transcriptome profiling is therefore the sum of the cell-type-specific gene expression weighted by cell-type proportion in the given sample. Deconvolution of gene expression profiles allows to reconstruct the cellular composition of tissues. xCell is a robust computational method that converts gene expression profiles to enrichment scores of 64 immune and stroma cell types across samples. Here, we described the method, discuss correct usage, and demonstrate an analysis of a cohort of peripheral blood mononuclear cells (PBMC).
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Aran, D. (2020). Cell-Type Enrichment Analysis of Bulk Transcriptomes Using xCell. In: Boegel, S. (eds) Bioinformatics for Cancer Immunotherapy. Methods in Molecular Biology, vol 2120. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0327-7_19
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DOI: https://doi.org/10.1007/978-1-0716-0327-7_19
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Publisher Name: Humana, New York, NY
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