Table 2 Number of positives and negatives used for training, tuning, and testing each model
Model Number | Genomes Used in Training | Tissue | Negative Set | Positives (Training, Validation, Test) | Negatives (Training, Validation, Test) | Negatives:Positives (Training, Validation, Test) |
|---|---|---|---|---|---|---|
1 | mm10 | Brain | Flanking Regions | 21,594, 2416, 4576 | 35,640, 4018, 7440 | 1.65:1, 1.66:1, 1.63:1 |
2 | mm10 | Brain | OCRs in Other Tissues | 21,594, 2416, 4576 | 427,174, 70,504, 82,172 | 19.78:1, 29.18:1, 17.96:1 |
3 | mm10 | Brain | Large G/C- and Repeat-Matched | 21,594, 2416, 4576 | 175,912, 23,880, 32,008 | 8.15:1, 9.88:1, 6.99:1 |
4 | mm10 | Brain | Small G/C- and Repeat-Matched | 21,594, 2416, 4576 | 35,358, 4776, 6654 | 1.64:1, 1.98:1, 1.45:1 |
5 | mm10 | Brain | Dinucleotide-Shuffled OCRs | 21,594, 2416, 4576 | 215,940, 24,160, 45,760 | 10:1, 10:1, 10:1 |
6 | mm10 | Brain | Non-OCR Orths. of OCRs | 21,594, 2416, 4576 | 25,086, 3456, 4694 | 1.16:1, 1.43:1, 1.03:1 |
7 | mm10 | Liver | Non-OCR Orths. of OCRs | 32,498, 4032, 7752 | 22,890, 2994, 4434 | 1:1.42, 1:1.35, 1:1.75 |
8 | mm10, hg38, rheMac8, rn6 | Brain | Non-OCR Orths. of OCRs | 74,688, 9036, 15,266 | 111,206, 14,650, 19,688 | 1.49:1, 1.62:1, 1.29:1 |
9 | mm10, rheMac8, rn6 | Liver | Non-OCR Orths. of OCRs | 81,886, 10,428, 17,688 | 67,278, 8680, 14,544 | 1:1.22, 1:1.20, 1:1.22 |