Table 2 LIME-identified genes with supporting evidence for implication in Parkinson disease
From: Neural networks reveal novel gene signatures in Parkinson disease from single-nuclei transcriptomes
Gene | Cell type identified by LIME | Supporting evidence |
|---|---|---|
AK5 | DaNeurons | •Nominally significant gene-level rare variant association with PD (p-value = 4.25e-2, beta = 6.87) |
ARL17B | Astrocytes, microglia, oligodendrocytes | •Significant gene-level common variant association with PD (MAGMA p-value = 1.03e-8, z-statistic = 5.61) •Cell type cis-eQTL co-locolization with WNT3 (astrocytes: PP = 0.98, beta = 1.22; microglia: PP = 0.98, beta = 1.29; oligodendrocytes: PP = 0.98, beta = 1.41) |
BAG3 | Oligodendrocytes | •GWAS PD-associated gene (Nalls et al. 2019: p-value = 2.00e-11, beta = 0.0763) |
B2M | Microglia, oligodendrocytes, OPC | •Nominally significant gene-level common variant association with PD (MAGMA p-value = 2.55e-3, z-statistic = 2.8) |
CACNA2D3 | DaNeurons | •Nominally significant gene-level rare variant association with PD (p-value = 1.70e-3, beta = 3.77) |
CHORDC1 | Astrocytes, endothelial, microglia, oligo., OPC, pericytes | •Significant gene-level rare variant association with PD (p-value = 6.78e-8, beta = 8.73) |
CIRBP | Oligodendrocytes | •Nominally significant gene-level common variant association with PD (MAGMA p-value = 3.03e-2, z-statistic = 1.88) |
CRYAB | Astrocytes, endothelial, microglia, oligo., OPC, pericytes, neurons | •Nominally significant gene-level common variant association with PD (MAGMA p-value = 2.96e-2, z-statistic = 1.89) |
GPC6 | DaNeurons | •Significant gene-level rare variant association with PD (p-value = 7.67e-8, beta = 16.46) |
MOBP | Microglia, oligodendrocytes | •Nominally significant gene-level common variant association with PD (MAGMA p-value = 9.27e-3, z-statistic = 2.35) |
PAM | DaNeurons | •GWAS PD-associated gene (Nalls et al. 2019: p-value = 2.00e-09, beta = 0.0621) |
SEMA5A | Neurons, DaNeurons | •Nominally significant gene-level rare variant association with PD (p-value = 2.23e-3, beta = 4.62) |
SIPA1L2 | Oligodendrocytes | •GWAS PD-associated gene (Nalls et al. 2019: p-value = 7.00e-17, beta = 0.1114; Kim et al. 2023: p-value = 1.00e-17, beta = 0.0269) |
RIMS1 | Astrocytes | •GWAS PD-associated gene (Nalls et al. 2019: p-value = 2.00e-10, beta = 0.0657; Kim et al. 2023: p-value = 7.00e-12, beta = 0.0208) |
TMEM163 | Microglia | •GWAS PD-associated gene (Nalls et al. 2019: p-value = 5.00e-14, beta = 0.0807; Kim et al. 2023: p-value = 5.00e-12, beta = 0.0400) •Nominally significant gene-level common variant association with PD (MAGMA p-value = 1.81e-3, z-statistic = 2.91) •Cell type cis-eQTL co-locolization with TMEM163 (microglia: PP = 0.99, beta = -0.47) |
