Fig. 5: Correlative mapping of ‘omic’ datasets reveals transcriptional upregulation of Rab27b and enriched diseases.

a Correlative analysis between RNA-Seq and the whole cell proteome reveals upregulation of a specific cohort of proteins. Scatter plot of VPS35 KO/VPS35-GFP RNA-Seq transcript abundances (x-axis) versus the protein abundances in the whole cell proteome (y-axis). Datapoints are coloured based on p-value scores in each experiment (green—significantly altered in whole cell proteome, magenta—significantly altered in RNA-Seq, blue—significantly altered in whole cell proteome and RNA-Seq), derived from two-tailed paired t tests. b–e Western blot and quantification of Rab27b protein levels in the whole cell lysates (b, c) and lysosomes (d, e) of wild-type, VPS35 KO, or VPS35-GFP rescue expression lines. Means ± SEM, one-sample two-tailed t tests with Holm–Šídák correction. For (c), adjusted p = 0.0082 (VPS35 KO Cl.15), 0.1603 (Cl.15 + VPS35-GFP). n = 4 independent repeats. For (e) p = 0.162 (VPS35 KO Cl.15), 0.0537 (VPS35 KO Cl.16), 0.2932 (VPS35 KO Cl.15 + VPS35-GFP), 0.162 (VPS35 KO Cl.16 + VPS35-GFP), data representative of 6 (wild type, VPS35 KO Cl.16 and VPS35 KO Cl.16 + VPS35 −GFP) and 4 (VPS35 KO Cl.15 and VPS35 KO Cl.15 + VPS35-GFP) independent repeats. kDa = kilodaltons. f Circos plot of overlap of significantly enriched proteins in VPS35 KO samples compared to both wild-type and VPS35-GFP-expressing rescue cells across all datasets. g, h Pathway enrichment meta-analysis of significantly enriched categories (g) and associated DisGeneNET categories (h) in VPS35 KO cells compared to both wild-type and VPS35-GFP-expressing rescue cells across all datasets, hypergeometric test. Datasets coloured to represent proteins significantly enriched in VPS35 KO: green—surface proteome, magenta—RNA-Seq transcriptome, orange—whole cell proteome, red—LysoIP proteome, blue—growth media ‘secretome’ proteome.