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).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Aran D, Sirota M, Butte AJ (2015) Systematic pan-cancer analysis of tumour purity. Nat Commun 6:8971. https://doi.org/10.1038/ncomms9971
Galon J, Costes A, Sanchez-Cabo F et al (2006) Type, density, and location of immune cells within human colorectal tumors predict clinical outcome. Sci (New York, NY) 313:1960–1964. https://doi.org/10.1126/science.1129139
Carr EJ, Dooley J, Garcia-Perez JE et al (2016) The cellular composition of the human immune system is shaped by age and cohabitation. Nat Immunol 17:461–468. https://doi.org/10.1038/ni.3371
Binnewies M, Roberts EW, Kersten K et al (2018) Understanding the tumor immune microenvironment (TIME) for effective therapy. Nat Med 24:541–550. https://doi.org/10.1038/s41591-018-0014-x
Aran D, Butte AJ (2016) Digitally deconvolving the tumor microenvironment. Genome Biol 17:175. https://doi.org/10.1186/s13059-016-1036-7
Aran D, Hu Z, Butte AJ (2017) xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biol 18:220. https://doi.org/10.1186/s13059-017-1349-1
Barbie DA, Tamayo P, Boehm JS et al (2009) Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature 462:108–112. https://doi.org/10.1038/nature08460
Bhattacharya S, Andorf S, Gomes L et al (2014) ImmPort: disseminating data to the public for the future of immunology. Immunol Res 58:234–239. https://doi.org/10.1007/s12026-014-8516-1
Whiting CC, Siebert J, Newman AM et al (2015) Large-scale and comprehensive immune profiling and functional analysis of normal human aging. PLoS One 10:e0133627. https://doi.org/10.1371/journal.pone.0133627
Aran D, Looney AP, Liu L et al (2019) Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol 20:163–172. https://doi.org/10.1038/s41590-018-0276-y
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
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
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0327-7_19
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0326-0
Online ISBN: 978-1-0716-0327-7
eBook Packages: Springer Protocols