Table 1 Summary of GWAS analyses of L. reuteri rodent adaptation genes. The rows show experimentally verified L. reuteri adaptation genes and columns all tested mGWAS tools. There are three measures of success that were chosen: Benjamini–Hochberg method, Bonferroni adjustment and rank in the sorted results. The pipe symbol (✔) indicates that the genes were identified as significant
From: aurora: a machine learning gwas tool for analyzing microbial habitat adaptation
Colonization factor | Measure | Scoarya | Fixed effects | Linear mixed effects | Elastic netb | Simultaneous | Subsequent | Synchronous | PhyC | aurora |
|---|---|---|---|---|---|---|---|---|---|---|
ure operon | Benjamini-Hochberg | ✔ | ✔ | X | NA | X | ✔ | ✔ | X | NA |
Bonferroni | ✔ | ✔ | X | NA | X | ✔ | ✔ | X | NA | |
Rank | 1324.5 | 14.5 | 34.5 | 10.5 | 28.5 | 10.5 | 29.5 | NaN | 9.5 | |
Serine-Rich Repeat Protein (SRRP) | Benjamini-Hochberg | ✔ | ✔ | X | NA | X | ✔ | X | X | NA |
Bonferroni | ✔ | ✔ | X | NA | X | ✔ | X | X | NA | |
Rank | 285 | 4 | 513 | 17 | 140.5 | 16 | 246 | 3016 | 18 | |
SecA2-SecY2 pathway | Benjamini-Hochberg | ✔ | ✔ | X | NA | X | X | X | X | NA |
Bonferroni | ✔ | ✔ | X | NA | X | X | X | X | NA | |
Rank | 1504.5 | 133.5 | 3086.5 | 41 | 4877 | 52.5 | 2642.5 | NaN | 32.5 | |
Glutaminase (glsA_1) | Benjamini-Hochberg | ✔ | X | X | NA | X | X | ✔ | X | NA |
Bonferroni | ✔ | X | X | NA | X | X | ✔ | X | NA | |
Rank | 2143.5 | 1994.5 | 685 | 143.5 | 140.5 | 74.5 | 64 | 301 | 41.5 |