Table 5.
Linear Mixed-Effects Modeling of Diet-Dependent Alterations in the FARMM Study Comparing Omnivore With Either EEN or Vegan Diets in the Relative Abundance of Genes in the cai Operon
| KEGG Orthology Identifier | Gene name | Term | Value | SE | Degrees of Freedom | t value | P value | FDR |
|---|---|---|---|---|---|---|---|---|
| K02182 | caiC | Study group vegan | -6.64 | 2.05 | 15 | -3.24 | .00 | 0.012 |
| K02182 | caiC | Study group EEN | -9.09 | 2.04 | 15 | -4.45 | .00 | 0.00036 |
| K02182 | caiC | Study group vegan: study day | 0.43 | 0.15 | 101 | 2.87 | .00 | 0.017 |
| K02182 | caiC | Study group EEN: study day | 0.52 | 0.15 | 101 | 3.48 | .00 | 0.0019 |
| K05245 | caiT | Study group vegan | -5.55 | 1.93 | 25 | -2.87 | .01 | 0.014 |
| K05245 | caiT | Study group EEN | -8.04 | 1.93 | 25 | -4.17 | .00 | 0.00056 |
| K05245 | caiT | Study group vegan: study day | 0.34 | 0.14 | 101 | 2.42 | .02 | 0.03 |
| K05245 | caiT | Study group EEN: study day | 0.40 | 0.14 | 101 | 2.80 | .01 | 0.011 |
| K08277 | caiF | Study group vegan | -6.26 | 2.10 | 25 | -2.97 | .01 | 0.014 |
| K08277 | caiF | Study group EEN | -8.00 | 2.10 | 25 | -3.82 | .00 | 0.0011 |
| K08277 | caiF | Study group vegan: study day | 0.39 | 0.16 | 101 | 2.50 | .01 | 0.03 |
| K08277 | caiF | Study group EEN: study day | 0.39 | 0.15 | 101 | 2.54 | .01 | 0.018 |
| K08279 | caiE | Study group vegan | -6.98 | 1.95 | 25 | -3.58 | .00 | 0.01 |
| K08279 | caiE | Study group EEN | -9.43 | 1.94 | 25 | -4.85 | .00 | 0.00028 |
| K08279 | caiE | Study group vegan: study day | 0.45 | 0.14 | 101 | 3.13 | .00 | 0.016 |
| K08279 | caiE | Study group EEN: study day | 0.49 | 0.14 | 101 | 3.46 | .00 | 0.0019 |
| K08297 | caiA | Study group vegan | -5.59 | 2.29 | 25 | -2.44 | .02 | 0.022 |
| K08297 | caiA | Study group EEN | -6.50 | 2.28 | 25 | -2.86 | .01 | 0.0085 |
| K08297 | caiA | Study group vegan: study day | 0.35 | 0.17 | 101 | 2.02 | .05 | 0.048 |
| K08298 | caiB | Study group vegan | -5.26 | 1.95 | 25 | -2.69 | .01 | 0.017 |
| K08298 | caiB | Study group EEN | -9.17 | 1.95 | 25 | -4.71 | .00 | 0.00028 |
| K08298 | caiB | Study group vegan: study day | 0.33 | 0.14 | 101 | 2.28 | .02 | 0.034 |
| K08298 | caiB | Study group EEN: study day | 0.53 | 0.14 | 101 | 3.65 | .00 | 0.0019 |
| K08299 | caiD | Study group vegan | -5.10 | 2.05 | 25 | -2.49 | .02 | 0.022 |
| K08299 | caiD | Study group EEN | -6.30 | 2.04 | 25 | -3.09 | .00 | 0.0057 |
| K08299 | caiD | Study group vegan: study day | 0.30 | 0.15 | 101 | 2.01 | .05 | 0.048 |
FDR, false discovery rate. For additional details see Figure 3C.