Table 2 Differential analysis on predicted expression datasets. Top unique differentially expressed genes upregulated in lesional skin compared with those in non-lesional skin when ranked according to log2-fold-change in (a) original dataset, (b) predicted dataset with 60 % observability and (c) sparse known-value (checkpoint) dataset without prediction at 60 % observability
From: Gene expression prediction using low-rank matrix completion
| Â | Â | Original dataset | Â | Â | Â | Recovered dataset (60 %) | Â | Â | Â | Checkpoint dataset (60 %) | Â | Â |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene | Probe ID | Symbol FC | log | Adj. | Probe ID | Symbol | log FC | Adj. | Probe ID | Symbol | log FC | Adj. |
ranking |  |  |  | P-Value ×10−10 |  |  |  | P-Value ×10−10 |  |  |  | P-Value |
1 | 205863_at | S100A12 | 9.79929 | < 1 | 205863_at | S100A12 | 8.99648 | < 1 | 211906_s_at | SERPINB4 | 6.21118 | 3.3×10−10 |
2 | 211906_s_at | SERPINB4 | 9.60376 | < 1 | 211906_s_at | SERPINB4 | 8.67119 | < 1 | 205863_at | S100A12 | 5.48282 | 3.3×10−9 |
3 | 205513_at | TCN1 | 8.65788 | < 1 | 205513_at | TCN1 | 8.12271 | < 1 | 205513_at | TCN1 | 5.07988 | 4.8×10−9 |
4 | 232220_at | S100A7A | 8.21988 | < 1 | 232220_at | S100A7A | 7.92112 | < 1 | 204385_at | KYNU | 5.06729 | 3.3×10−10 |
5 | 205660_at | OASL | 7.94647 | < 1 | 205660_at | OASL | 7.4045 | < 1 | 1569555_at | GDA | 4.75835 | 4.8×10−9 |
6 | 220664_at | SPRR2C | 7.87929 | < 1 | 220664_at | SPRR2C | 7.3366 | < 1 | 205844_at | VNN1 | 4.70129 | 3.3×10−10 |
7 | 207602_at | TMPRSS11D | 7.64471 | < 1 | 1569555_at | GDA | 7.11896 | < 1 | 209719_at | SERPINB3 | 4.67529 | 1.6×10−4 |
8 | 1569555_at | GDA | 7.39506 | < 1 | 207602_at | TMPRSS11D | 7.10503 | < 1 | 234699_at | RNASE7 | 4.57012 | 2.9×10−7 |