Differential gene and isoform expression using cell type proportions as covariates.

Shown is the differential expression analysis for both genes and isoforms performed using ridge regression and cell type proportions as covariates between: iPSC-CVPC and adult heart; iPSC-CVPC and adult arteria; adult heart and adult arteria. For each gene and isoform, we report: isoform ID, gene ID and gene name; the tested tissues (tissue 1 and tissue 2); the covariate, including “tissue”, which represents the differential expression between tissue 1 and tissue 2, and each of the cell types; effect size, standard error, p-value and FDR correction (Bonferroni). Only significant associations (FDR < 0.05) are reported. All tests can be found at https://doi.org/10.6084/m9.figshare.13537343. The associations between fibroblast and immune cell type proportion and developmental stage (iPSC-CVPC vs. adult heart) are likely noisy, because these two cell types were not present in iPSC-CVPCs. Therefore the genes and isoforms associated with these two cell types were not considered in the count of genes and isoforms associated with both developmental stage and cell types in the ridge regression analysis.
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