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Table 2 Top 20 ranking genes by feature importance for predicting RA and SLE in proposed models

From: Machine learning approaches for the genomic prediction of rheumatoid arthritis and systemic lupus erythematosus

Model Gradient tree boosting Extreme gradient boosting
Rank SNP Gene Symbol Feature Importance SNP Gene Symbol Feature Importance
1 rs6906021 HLA-DQA1 0.1205 rs34965214 HLA-DQA1 0.0998
2 rs9271858 HLA-DRB1 0.1030 rs3104376 HLA-DQA1 0.0562
3 rs9273505 HLA-DQB1 0.0895 rs1391371 HLA-DQA1 0.0557
4 Affx-28,477,341 HLA-DRB5 0.0848 rs9271662 HLA-DRB1 0.0494
5 rs4999342 HLA-DRB5 0.0741 rs9273322 HLA-DQA1 0.0387
6 rs41269945 HLA-DQA1 0.0452 rs1049072 HLA-DQB1 0.0380
7 rs3104376 HLA-DQA1 0.0372 rs9274605 HLA-DQB1 0.0359
8 rs9274605 HLA-DQB1 0.0348 rs9273370 HLA-DQA1 0.0345
9 rs2395533 HLA-DQA1 0.0323 rs17843604 HLA-DQA1 0.0337
10 rs9274655 HLA-DQB1 0.0317 rs9271850 HLA-DRB1 0.0269
11 rs9271662 HLA-DRB1 0.0239 rs9271588 HLA-DRB1 0.0241
12 rs3830059 HLA-DQB1 0.0224 rs9271425 HLA-DRB1 0.0220
13 rs200716952 HLA-DQB2 0.0207 rs4999342 HLA-DRB5 0.0211
14 rs1003879 C6orf10 0.0201 rs9469219 HLA-DQB1 0.0210
15 rs9271489 HLA-DRB1 0.0194 rs9271858 HLA-DRB1 0.0177
16 rs9272461 HLA-DQA1 0.0166 rs9275087 HLA-DQB1 0.0173
17 Affx-28,498,545 HLA-DQB1 0.0137 rs17843619 HLA-DQA1 0.0165
18 rs2395111 NOTCH4 0.0135 rs17843605 HLA-DQA1 0.0162
19 rs1049072 HLA-DQB1 0.0124 rs9273505 HLA-DQB1 0.0159
20 Affx-28,494,632 HLA-DQA1 0.0121 rs2894249 C6orf10 0.0158
  1. SNP: single nucleotide polymorphism