Table 1.
The 47 genes selected as significantly up-regulated by ALDEx2 when using the NFκB subunits as a reference
| Gene | Effect size | Difference (between) | Difference (within) | Expected Benjamini-Hochberg P-value |
|---|---|---|---|---|
| Il1b | 4.7372 | 3.9576 | 0.6912 | 0.0000 |
| Irg1 | 4.3462 | 3.8904 | 0.7888 | 0.0000 |
| Il1a | 3.5950 | 3.8242 | 0.9037 | 0.0000 |
| Cd40 | 2.2887 | 5.3325 | 2.0422 | 0.0000 |
| Ifih1 | 2.2056 | 2.8529 | 1.1157 | 0.0000 |
| Isg15 | 1.9678 | 4.4490 | 1.8330 | 0.0000 |
| Oasl1 | 1.9304 | 5.6562 | 2.1200 | 0.0000 |
| Ifit1 | 1.8317 | 5.6101 | 2.0773 | 0.0000 |
| Ptgs2 | 1.6923 | 4.0869 | 2.0606 | 0.0002 |
| Gbp5;Gbp1 | 1.6523 | 2.4494 | 1.2349 | 0.0000 |
| Rsad2 | 1.4933 | 6.2747 | 2.4692 | 0.0001 |
| Marcksl1 | 1.4886 | 1.0748 | 0.5740 | 0.0001 |
| BC006779 | 1.4686 | 2.2184 | 1.2465 | 0.0001 |
| Mndal | 1.4163 | 2.1047 | 1.5182 | 0.0000 |
| Parp14 | 1.3139 | 1.7655 | 0.9357 | 0.0002 |
| Ifi205 | 1.2916 | 5.3159 | 3.4587 | 0.0026 |
| Slc7a2 | 1.2883 | 1.3797 | 0.9920 | 0.0002 |
| Ifit2 | 1.2292 | 5.4975 | 2.6744 | 0.0002 |
| Clic4 | 1.2037 | 0.8486 | 0.5765 | 0.0003 |
| Sp140 | 1.1612 | 1.0030 | 0.7385 | 0.0005 |
| Cmpk2 | 1.1149 | 5.7323 | 2.1088 | 0.0003 |
| Stat5a | 1.0806 | 0.8666 | 0.6461 | 0.0017 |
| Ifi47 | 1.0443 | 2.0495 | 1.5704 | 0.0030 |
| Pyhin1 | 1.0152 | 1.9150 | 1.4752 | 0.0024 |
| Ifit3 | 0.9978 | 4.7313 | 3.2116 | 0.0012 |
| Ccl5 | 0.9962 | 2.0765 | 1.6671 | 0.0015 |
| Acsl1 | 0.9937 | 1.0837 | 1.0073 | 0.0009 |
| Il1rn | 0.9811 | 0.6795 | 0.6366 | 0.0017 |
| Irgm1 | 0.9755 | 1.7076 | 1.0634 | 0.0094 |
| IIGP;Iigp1 | 0.9588 | 3.5610 | 3.1760 | 0.0023 |
| Rnf213;AK217856 | 0.9541 | 1.2867 | 1.0478 | 0.0041 |
| Daxx | 0.9118 | 1.1938 | 0.9013 | 0.0119 |
| Flnb | 0.8639 | 1.6654 | 1.8185 | 0.0122 |
| Cd274 | 0.8299 | 0.6050 | 0.6354 | 0.0051 |
| Trex1 | 0.8171 | 0.5647 | 0.6350 | 0.0090 |
| Car13 | 0.7586 | 1.1455 | 1.2839 | 0.0140 |
| Xaf1 | 0.7550 | 1.5118 | 1.4338 | 0.0214 |
| Gbp3 | 0.7478 | 1.5118 | 1.4837 | 0.0128 |
| Ehd1 | 0.7460 | 0.3648 | 0.4812 | 0.0078 |
| Gm4902 | 0.7413 | 1.9614 | 1.7899 | 0.0151 |
| Rasa4 | 0.7254 | 0.8805 | 0.9109 | 0.0478 |
| Oas3 | 0.7089 | 1.5673 | 1.7756 | 0.0213 |
| Serpinb2 | 0.7048 | 1.7770 | 2.1734 | 0.0272 |
| Dhx58;D11lgp2 | 0.6947 | 1.4875 | 1.6956 | 0.0425 |
| Gbp2 | 0.6597 | 1.5376 | 1.7339 | 0.0212 |
| Saa3 | 0.6291 | 1.0259 | 1.5384 | 0.0187 |
| Sbds | 0.5522 | 0.3107 | 0.5363 | 0.0443 |
One can interpret this “up-regulation” to mean that the gene increases its expression in response to LPS stimulation more than NFκB. All P-values correspond to the expectation of the Benjamini-Hochberg adjusted P-values computed from a Welch’s t-test over 128 simulated instances of the data. By choosing a reference that is relevant to the biological system under study, we can gain meaningful insights from the data without any need for normalization. In this table, between-group differences are the differences between the 2 conditions (defined for each Dirichlet instance), within-group differences are the maximum difference across Dirichlet instances (defined for each condition), and effect sizes are the ratio of the between-group differences to the maximum of within-group differences (defined for each Dirichlet instance). The columns “Effect size,” “Difference (between),” and “Difference (within)” report the median effect size, median between-group difference, and median within-group difference, respectively.