Table 3 Effects of varying feature sizes on all the Test-3 dataset when k-mer size is 3 for the forward feature set
From: A novel feature extraction method based on highly expressed SNPs for tissue-specific gene prediction
Tissue | Feature size | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
[6, 7, 8] | [7, 8, 9] | [8, 9, 10] | [9, 10, 11] | [10, 11, 12] | ||||||
Acc | F1 | Acc | F1 | Acc | F1 | Acc | F1 | Acc | F1 | |
Adipose subcutaneous | 0.84 | 0.80 | 0.93 | 0.91 | 0.97 | 0.97 | 0.99 | 0.99 | 0.99 | 0.99 |
Adipose visceral omentum | 0.87 | 0.84 | 0.95 | 0.94 | 0.98 | 0.97 | 0.99 | 0.99 | 0.99 | 0.99 |
Adrenal gland | 0.91 | 0.89 | 0.96 | 0.95 | 0.98 | 0.98 | 0.99 | 0.99 | 1.00 | 1.00 |
Artery aorta | 0.86 | 0.83 | 0.95 | 0.93 | 0.98 | 0.97 | 0.99 | 0.98 | 0.99 | 0.99 |
Artery coronary | 0.94 | 0.92 | 0.98 | 0.97 | 0.99 | 0.99 | 1.00 | 0.99 | 1.00 | 1.00 |
Artery tibial | 0.84 | 0.81 | 0.93 | 0.92 | 0.97 | 0.96 | 0.99 | 0.98 | 0.99 | 0.99 |
Brain amygdala | 0.96 | 0.96 | 0.98 | 0.98 | 0.99 | 0.99 | 1.00 | 1.00 | 1.00 | 1.00 |
Brain anterior cingulate cortex | 0.94 | 0.93 | 0.97 | 0.97 | 0.99 | 0.99 | 1.00 | 0.99 | 1.00 | 1.00 |
Brain caudate basal ganglia | 0.92 | 0.90 | 0.97 | 0.96 | 0.99 | 0.98 | 0.99 | 0.99 | 1.00 | 1.00 |
Brain cerebellar hemisphere | 0.90 | 0.88 | 0.96 | 0.95 | 0.98 | 0.98 | 0.99 | 0.99 | 1.00 | 0.99 |
Brain cerebellum | 0.88 | 0.85 | 0.96 | 0.95 | 0.98 | 0.98 | 0.99 | 0.99 | 1.00 | 0.99 |
Brain cortex | 0.91 | 0.89 | 0.97 | 0.96 | 0.99 | 0.98 | 0.99 | 0.99 | 1.00 | 1.00 |
Brain frontal cortex | 0.93 | 0.91 | 0.97 | 0.96 | 0.99 | 0.98 | 0.99 | 0.99 | 1.00 | 1.00 |
Brain hippocampus | 0.94 | 0.93 | 0.98 | 0.98 | 0.99 | 0.99 | 1.00 | 0.99 | 1.00 | 1.00 |
Brain hypothalamus | 0.95 | 0.93 | 0.98 | 0.97 | 0.99 | 0.99 | 1.00 | 1.00 | 1.00 | 1.00 |
Brain nucleus accumbens basal ganglia | 0.92 | 0.90 | 0.97 | 0.96 | 0.99 | 0.99 | 0.99 | 0.99 | 1.00 | 1.00 |
Brain putamen basal ganglia | 0.93 | 0.91 | 0.98 | 0.97 | 0.99 | 0.99 | 1.00 | 0.99 | 1.00 | 1.00 |
Brain spinal cord cervical | 0.96 | 0.95 | 0.98 | 0.98 | 0.99 | 0.99 | 1.00 | 1.00 | 1.00 | 1.00 |
Brain substantia nigra | 0.97 | 0.96 | 0.99 | 0.98 | 0.99 | 0.99 | 1.00 | 1.00 | 1.00 | 1.00 |
Breast mammary | 0.89 | 0.86 | 0.95 | 0.94 | 0.98 | 0.98 | 0.99 | 0.99 | 1.00 | 0.99 |
Cells cultured fibroblasts | 0.84 | 0.81 | 0.93 | 0.92 | 0.97 | 0.97 | 0.99 | 0.98 | 0.99 | 0.99 |
Cells EBV transformed lymphocytes | 0.94 | 0.93 | 0.98 | 0.97 | 0.99 | 0.99 | 1.00 | 0.99 | 1.00 | 1.00 |
Colon sigmoid | 0.89 | 0.86 | 0.96 | 0.94 | 0.98 | 0.97 | 0.99 | 0.99 | 0.99 | 0.99 |
Colon transverse | 0.88 | 0.85 | 0.95 | 0.93 | 0.98 | 0.97 | 0.99 | 0.99 | 1.00 | 0.99 |
Esophagus gastroesophageal junction | 0.89 | 0.86 | 0.96 | 0.95 | 0.98 | 0.98 | 0.99 | 0.99 | 0.99 | 0.99 |
Esophagus mucosa | 0.85 | 0.82 | 0.94 | 0.92 | 0.97 | 0.97 | 0.99 | 0.98 | 0.99 | 0.99 |
Esophagus muscularis | 0.85 | 0.82 | 0.94 | 0.93 | 0.98 | 0.97 | 0.99 | 0.98 | 0.99 | 0.99 |
Heart atrial appendage | 0.88 | 0.86 | 0.95 | 0.94 | 0.98 | 0.97 | 0.99 | 0.99 | 1.00 | 0.99 |
Heart left ventricle | 0.91 | 0.88 | 0.96 | 0.95 | 0.98 | 0.98 | 0.99 | 0.99 | 1.00 | 1.00 |
Kidney cortex | 0.99 | 0.99 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
Liver | 0.94 | 0.92 | 0.97 | 0.97 | 0.99 | 0.98 | 1.00 | 1.00 | 1.00 | 1.00 |
Lung | 0.86 | 0.82 | 0.94 | 0.93 | 0.98 | 0.97 | 0.99 | 0.98 | 0.99 | 0.99 |
Minor salivary gland | 0.95 | 0.94 | 0.98 | 0.97 | 0.99 | 0.99 | 1.00 | 0.99 | 1.00 | 1.00 |
Muscle skeletal | 0.86 | 0.82 | 0.94 | 0.92 | 0.98 | 0.97 | 0.99 | 0.99 | 0.99 | 0.99 |
Nerve tibial | 0.82 | 0.78 | 0.92 | 0.90 | 0.97 | 0.96 | 0.99 | 0.98 | 0.99 | 0.99 |
Ovary | 0.94 | 0.93 | 0.98 | 0.97 | 0.99 | 0.99 | 1.00 | 1.00 | 1.00 | 1.00 |
Pancreas | 0.90 | 0.87 | 0.96 | 0.95 | 0.98 | 0.98 | 0.99 | 0.99 | 1.00 | 0.99 |
Pituitary | 0.91 | 0.88 | 0.96 | 0.95 | 0.99 | 0.98 | 0.99 | 0.99 | 1.00 | 1.00 |
Prostate | 0.93 | 0.91 | 0.97 | 0.97 | 0.99 | 0.98 | 1.00 | 0.99 | 1.00 | 1.00 |
Skin not sun exposed suprapubic | 0.84 | 0.80 | 0.93 | 0.92 | 0.97 | 0.96 | 0.99 | 0.98 | 0.99 | 0.99 |
Skin sun exposed lower leg | 0.84 | 0.80 | 0.93 | 0.91 | 0.97 | 0.96 | 0.99 | 0.98 | 0.99 | 0.99 |
Small intestine terminal ileum | 0.94 | 0.92 | 0.98 | 0.97 | 0.99 | 0.99 | 1.00 | 0.99 | 1.00 | 1.00 |
Spleen | 0.89 | 0.86 | 0.95 | 0.94 | 0.98 | 0.98 | 0.99 | 0.99 | 1.00 | 0.99 |
Stomach | 0.91 | 0.88 | 0.96 | 0.95 | 0.98 | 0.98 | 0.99 | 0.99 | 1.00 | 1.00 |
Testis | 0.83 | 0.79 | 0.93 | 0.91 | 0.97 | 0.96 | 0.99 | 0.98 | 0.99 | 0.99 |
Thyroid | 0.82 | 0.78 | 0.92 | 0.90 | 0.97 | 0.96 | 0.98 | 0.98 | 0.99 | 0.99 |
Uterus | 0.96 | 0.95 | 0.99 | 0.98 | 0.99 | 0.99 | 1.00 | 1.00 | 1.00 | 1.00 |
Vagina | 0.97 | 0.96 | 0.99 | 0.98 | 0.99 | 0.99 | 1.00 | 1.00 | 1.00 | 1.00 |
Whole blood | 0.86 | 0.83 | 0.94 | 0.93 | 0.98 | 0.97 | 0.99 | 0.99 | 0.99 | 0.99 |
MEAN | 0.90 | 0.88 | 0.96 | 0.95 | 0.98 | 0.98 | 0.99 | 0.99 | 1.00 | 0.99 |
STDEV | 0.05 | 0.06 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 |
MIN | 0.82 | 0.78 | 0.92 | 0.90 | 0.97 | 0.96 | 0.98 | 0.98 | 0.99 | 0.99 |
MAX | 0.99 | 0.99 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |