Fig. 1

Tau-triggered differentially expressed genes. a Gene expression heatmap showing replicate samples from control flies (elav, n = 3) and elav > Tau^WT (Tau^WT, n = 3) grouped by age (1-, 10-, and 20-days). Columns denote individual samples. Rows consist of clustered, normalized expression values for all differentially-expressed transcripts (n = 1653, FDR < 0.05) based on the joint regression model adjusting for age. Each column represents an individual sample. In both control and Tau^WT animals, age is the dominant driver of gene expression patterns. b Gene expression heatmap showing replicate samples from batch-matched control flies (elav, n = 2) and elav > Tau^R406W (Tau^R406W, n = 3). Rows consist of clustered, normalized expression values for all differentially-expressed transcripts (n = 4992, FDR < 0.05) based on the joint regression model adjusting for age. While age remains a major driver, Tau^R406W has a more substantial and appreciable impact on expression pattern compared with Tau^WT (a, above). c Plot (top) showing Tau^R406W-triggered log₂ fold-change (LFC) in the transcriptome and proteome. The plot only includes those genes detected as both transcripts and proteins and also differentially expressed (n = 1477, FDR < 0.05), based on the joint regression model including longitudinal data and adjusting for age. Colors denote whether the gene was differentially expressed in the transcriptome (unfilled), proteome (blue), or both (orange). Quadrants I and III include gene expression changes that are concordant (same direction) at the transcript and protein level; whereas quadrants II and IV depict discordant changes. A substantial proportion of differentially-expressed transcripts or proteins are discordant (table, bottom). See Fig. 2 and Additional file 1: Figure S8 for selected examples (labeled)