Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data.
Ontology highlight
ABSTRACT:
SUBMITTER: Racle J
PROVIDER: S-EPMC5718706 | biostudies-literature | 2017 Nov
REPOSITORIES: biostudies-literature
Publications
Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data.
Racle Julien J de Jonge Kaat K Baumgaertner Petra P Speiser Daniel E DE Gfeller David D
eLife 20171113
Immune cells infiltrating tumors can have important impact on tumor progression and response to therapy. We present an efficient algorithm to simultaneously estimate the fraction of cancer and immune cell types from bulk tumor gene expression data. Our method integrates novel gene expression profiles from each major non-malignant cell type found in tumors, renormalization based on cell-type-specific mRNA content, and the ability to consider uncharacterized and possibly highly variable cell types ...[more]
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