ConfoundR is an interactive web application that enable users to:
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Compare the expression of an individual gene in tumour epithelium with the expression of the same gene in stromal/non-epithelial cells
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Compare the expression of multiple genes in tumour epithelium with the expression of the same genes in stromal/non-epithelial cells
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Compare the expression/enrichment of a gene set/gene signature in tumour epithelium with the expression/enrichment of the same gene set/gene signature in stromal/non-epithelial cells
in datasets in which tumours have been separated by laser capture microdissection (LCM) or fluorescence-activated cell sorting (FACS) into their constituent cell populations and the constituent populations have been separately transcriptionally profiled.
By enabling the above comparisons the app enables users to identify individual genes, or gene sets/gene signatures that show differential expression/enrichment across tumour cell populations and that therefore may be confounded when examined in bulk transcriptomic tumour samples as a consequence of different proportions of tumour cell populations.
The ConfoundR application is freely available at: https://confoundr.qub.ac.uk