| Category | Feature | Feature Details | Count | Type | Tools |
|---|---|---|---|---|---|
| DNA Sequence | K-mers and autocorrelation features | 259 | Numerical | rDNAse (R package) | |
| Protein Sequence | K-mers and autocorrelation features | 9858 | Numerical | protr package (R package) | |
| Sequence | Codon | Codon adaptation index (CAI) , Stacking Energy, Effective number of codons (Nc) etc | 14 | Numerical | SADEG |
| Protein Structure | Transmembrane domain, coils, loops etc | 5 | Numerical + Categorical | DisEMBL, TMHMM, and SignalP | |
| Protein Localization | Subcellular localizations | 17 | Categorical | WolfPsort and Deeploc | |
| Genomic Structure | Gene Structure | Exon number, gene length etc | 10 | Numerical + Categorical | Customized Python Script |
| Distance | Chromosomal distance, distance to nearest telomere etc | 4 | Numerical | Customized Python Script | |
| Expression | Gene Expression | Tissue expression, Tissue breadth, Maximum expression etc | 175 | Numerical | qTeller |
| Protein Expression | 26 | Numerical | qTeller | ||
| Chromatin States | Combination of histone modifications | 13 | Numerical | ||
| ATAC-Seq | Open chromatin peak | 6 | Numerical | ||
| Chromatin Interactions | Histone Modifications | ChIP-Seq peaks | 8 | Numerical | |
| DNA Methylation | CG, CHG, and CHH | 9 | Numerical | ||
| miRNA | 3 | Numerical | |||
| Insertions | 6 | Numerical | |||
| TF Binding Sites | 99 | Numerical | |||
| Count | Transcription Start Site | Counts of each Each category type cross three regions of the genome: within gene body, 1KB region directly upstream and downstream of the gene start site and 5KB region directly upstream and downstream of the gene start site. | 6 | Numerical | Bedtools and Customized Python Scripts |
| Enhancers | 6 | Numerical | |||
| Transposable Elements | 3 | Numerical | |||
| G-Quadruplex | 5 | Numerical | |||
| Gene interactions | Correlation | WGCNA modules | 12 | Categorical | |
| Variomic | SNP | WGCNA modules | 1 | Numerical | Bedtools |
| SNP Effect | WGCNA modules | 27 | Numerical | SnpEff | |
| Other | Evolutionary | Kn vs Ks, Gene Age | 9 | Numerical | phylostratr |
| Protein domains | Total PFAM per gene model /td> | 1 | Numerical | Customized Python Script |