Fig. 5: Characterization of filtered LIME-identified genes.

Heatmap characterizing the 66 unique genes included in the final LIME-identified gene set. The panels are arranged from bottom to top as follows: 1) Mean LIME feature importance Z-Scores: This panel shows the mean LIME feature importance Z-scores across all snRNAseq datasets. Grey tiles indicate genes that were not identified by LIME in the corresponding cell type. 2) Log2 fold-change: this panel shows the log2 fold-change between Parkinson disease (PD) and control cells across all snRNAseq datasets. Grey tiles indicate genes that were not identified by LIME in the corresponding cell type. 3) Cell type cis-expression quantitative trait loci (eQTL): this panel highlights LIME-identified genes that were identified as cell type cis-eQTLs by Bryois et al. Tiles marked with an “X” represent cell type cis-eQTLs that co-localized with PD-associated genes (posterior probability (PP) > 0.7). Grey tiles indicate genes that were not identified by LIME or were not identified as cis-eQTLs in the corresponding cell type. 4) PD genome-wide association analysis (GWAS): this panel highlights LIME-identified genes that showed an association with PD-risk by GWAS performed by Nalls et al. or Kim et al. Only genes that met genome wide significance (P < 5.00e-8) are shown. Grey tiles indicate genes that were not found to be significantly associated with PD in Nalls et al. (bottom) or Kim et al. (top). 5) Neurodegenerative Disease Knowledge Portal (NDKP) gene-level associations: this panel highlights LIME-identified genes that showed gene-level associations with various diseases in the NDKP cohorts. All nominally significant common and rare variant associations are shown. Tiles marked with an asterisk denote significant associations with the corresponding disease or a Human Genetic Evidence (HuGE) Score ≥ 3. Grey tiles indicate non-significant associations. DaNeurons dopaminergic neurons, OPC oligodendrocyte precursor cells.