Genetic control of the HDL proteome

Nathalie Pamir; Calvin Pan; Deanna L. Plubell; Patrick M. Hutchins; Chongren Tang; Jake Wimberger; Angela Irwin; Thomas Q. de Aguiar Vallim; Jay W. Heinecke; Aldons J. Lusis

Supplementary Figure 3 Hierarchical clustering of the HDL metrics: Proteome (normalized to total PSMs), sterol efflux, particle concentration and size. min.MF, plus.MF, delta.BHK are unstimulated, ABCA1 upregulated and ABCA1 specific sterol efflux from BHK cells respectively. min.cAMP, plus.cAMP, delta.J774 are unstimulated, ABCA1 upregulated and ABCA1 specific sterol efflux from J774 cells respectively. m.hdlp and t.hdlp are medium size and total HDL particle concentration. m.hdl.size and l.hdl.size are medium and large HDL sizes respectively. The correlation structure was determined using pearson correlation. The protein functional groups were curated from DAVID, KEGG, Panther, and Uniprot databases. Figure 1 : The heatmap visualization of the HDL protein abundances (calculated as normalized to total PSMs) across 93 strains. The proteins, their biological functions and cellular locations are represented. Logarithmic transformation of the total PSM normalized data has been performed to accommodate the abundance distribution form high (red) to very low (dark blue). White squares represent not available values. Both the proteins and the strains were clustered using Euclidean distances. Figure 3 . Hierarchical clustering of the HDL metrics: Proteome (normalized to total PSMs), sterol efflux, particle concentration and size. min.MF, plus.MF, delta.BHK are unstimulated, ABCA1 upregulated and ABCA1 specific sterol efflux from BHK cells respectively. min.cAMP, plus.cAMP, delta.J774 are unstimulated, ABCA1 upregulated and ABCA1 specific sterol efflux from J774 cells respectively. m.hdlp and t.hdlp are medium size and total HDL particle concentration. m.hdl.size and l.hdl.size are medium and large HDL sizes respectively. The correlation structure was determined using pearson correlation. The protein functional groups were curated from DAVID, KEGG, Panther, and Uniprot databases. Table 3 . Local adipose eQTL and local HDL pQTL. Table 4 . Potential causal interaction based on local pQTL analyses. . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/405811 doi: bioRxiv preprint