Searching for a specific cell type in TCGA
Hi all,
I was wondering if there is a way to search a specific cell type within "The Cancer Genome Atlas"? Like find epithelial in a type of cancer?
Thanks
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jabbari.parnian •
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Type of cancer but not a specific cell type since TCGA data was not done at cell level. Try cBioPortal for a high level exploration.
You can figure out what cancers arise from which cells by looking through cancer textbooks/literature. For example, lung adenocarcinoma arises from epithelial cells, sarcomas arise from connective tissue cells, while lymphomas arise from lymphocytes.
Note that, as genomax mentioned, the genomics data was done in bulk tissue (so there will be immune cells, stromal cells, etc. present in epithelial cancers). For gene expression data, you can try to resolve the individual member cell types with a deconvolution tool such as CIBERSORT.