Table 2.
Feature indices of RP genes.
| RP gene | Expression profile cluster | Amino acid encording cluster | Synonymous codon frequency cluster | TATA box (-40 bp ~ -21 bp) | Predicted Transcription factors bound | Feature Index |
| RPLP0 | S2 | O | M | Y | AP | 3.3 |
| RPS26 | O | O | M | Y | GC, AP | 3.2 |
| RPSA | M | O | S2 | N | AP | 2.3 |
| RPS29 | M | S2 | O | N | AP | 2.3 |
| RPL5 | M | M | S1 | N | AP | 2.3 |
| RPL14 | M | O | S2 | N | GC | 2.3 |
| RPLP1 | S1 | S1 | M | N | NRF, AP | 2.2 |
| RPLP2 | S1 | S1 | M | N | NRF, GC | 2.2 |
| RPL36A | M | S2 | M | Y | NRF, AP | 2.2 |
| RPS6 | - | M | S1 | N | NRF, GC, AP | 2.1 |
| RPS18 | S2 | M | M | Y | NRF, GC, AP | 2.1 |
| RPS27 | M | O | M | Y | GC, YY, AP | 2.1 |
| RPL28 | O | M | O | N | NRF, GC, AP | 2.1 |
| RPL41 | - | O | O | N | NRF, GC, AP | 2.1 |
| RPS3A | M | M | S1 | N | NRF, GC, YY, AP | 2.0 |
| RPS4Y | O | M | S1 | N | - | 2.0 |
| RPS28 | - | O | M | Y | NRF, GC, YY, AP | 2.0 |
| RPL4 | M | M | S1 | N | NRF, GC, YY, AP | 2.0 |
| RPL39 | M | S2 | O | N | NRF, GC, YY, AP | 2.0 |
| RPS15A | S2 | M | M | N | YY | 1.3 |
| RPS23 | M | M | S2 | N | GC | 1.3 |
| RPS24 | O | M | M | N | NRF | 1.3 |
| RPL6 | O | M | M | N | NRF | 1.3 |
| RPL7 | M | M | S2 | N | AP | 1.3 |
| RPL9 | - | M | S2 | N | AP | 1.3 |
| RPL37A | M | S2 | M | N | NRF | 1.3 |
| RPS15 | M | M | O | N | NRF, AP | 1.2 |
| RPS21 | - | O | M | N | GC, AP | 1.2 |
| RPL31 | O | M | M | N | NRF, GC | 1.2 |
| RPL32 | O | M | M | N | NRF, AP | 1.2 |
| RPL35 | O | M | M | N | GC, AP | 1.2 |
| RPL37 | - | S2 | M | N | NRF, AP | 1.2 |
| RPS2 | O | M | M | N | NRF, GC, AP | 1.1 |
| RPS3 | M | O | M | N | NRF, YY, AP | 1.1 |
| RPS5 | - | O | M | N | NRF, GC, AP | 1.1 |
| RPS12 | - | O | M | N | GC, YY, AP | 1.1 |
| RPS17 | O | M | M | N | NRF, GC, AP | 1.1 |
| RPS25 | - | M | S2 | N | NRF, GC, AP | 1.1 |
| RPL3 | M | M | O | N | NRF, GC, YY | 1.1 |
| RPL17 | M | M | S2 | N | NRF, YY, AP | 1.1 |
| RPL21 | M | M | S2 | N | GC, YY, AP | 1.1 |
| RPL29 | S2 | M | M | N | NRF, GC, AP | 1.1 |
| RPS13 | M | M | S2 | N | NRF, GC, YY, AP | 1.0 |
| RPS27A | M | M | S2 | N | NRF, GC, YY, AP | 1.0 |
| RPL10 | - | M | M | Y | NRF, GC, YY, AP | 1.0 |
| RPL27A | O | M | M | N | NRF, GC, YY, AP | 1.0 |
| RPS9 | - | M | M | N | AP | 0.3 |
| RPS11 | M | M | M | N | YY | 0.3 |
| RPL7A | M | M | M | N | GC | 0.3 |
| RPL13 | M | M | M | N | NRF | 0.3 |
| RPL13A | M | M | M | N | YY | 0.3 |
| RPL22 | M | M | M | N | GC | 0.3 |
| RPL34 | - | M | M | N | NRF | 0.3 |
| RPS7 | M | M | M | N | GC, AP | 0.2 |
| RPS10 | - | M | M | N | NRF, GC | 0.2 |
| RPS20 | M | M | M | N | GC, AP | 0.2 |
| RPS30 | M | M | M | N | GC, AP | 0.2 |
| RPL8 | M | M | M | N | NRF, AP | 0.2 |
| RPL10A | M | M | M | N | NRF, GC | 0.2 |
| RPL11 | M | M | M | N | NRF, GC | 0.2 |
| RPL12 | - | M | M | N | GC, AP | 0.2 |
| RPL18 | M | M | M | N | GC, AP | 0.2 |
| RPL23A | M | M | M | N | GC, YY | 0.2 |
| RPL26 | M | M | M | N | NRF, AP | 0.2 |
| RPL35A | - | M | M | N | GC, AP | 0.2 |
| RPS4X | M | M | M | N | NRF, GC, AP | 0.1 |
| RPS8 | M | M | M | N | GC, YY, AP | 0.1 |
| RPS16 | M | M | M | N | NRF, GC, AP | 0.1 |
| RPS19 | M | M | M | N | NRF, GC, AP | 0.1 |
| RPL15 | M | M | M | N | GC, YY, AP | 0.1 |
| RPL18A | - | M | M | N | NRF, YY, GC | 0.1 |
| RPL19 | M | M | M | N | NRF, GC, AP | 0.1 |
| RPL23 | M | M | M | N | NRF, GC, AP | 0.1 |
| RPL24 | M | M | M | N | NRF, YY, GC | 0.1 |
| RPL27 | - | M | M | N | NRF, GC, AP | 0.1 |
| RPL30 | M | M | M | N | NRF, YY, AP | 0.1 |
| RPL36 | - | M | M | N | NRF, YY, AP | 0.1 |
| RPL38 | M | M | M | N | NRF, GC, AP | 0.1 |
| RPL40 | M | M | M | N | GC, YY, AP | 0.1 |
| RPS14 | - | M | M | N | NRF, GC, YY, AP | 0.0 |
The feature index (FI) is a quantitative measure of the heterogeneity in an individual RP gene. Expression profile, amino acids encoded, and synonymous codon composition: a value of 1 was given to genes that did not belong to the Main cluster. TATA box: a value of 1 was given to genes that had TATA boxes. Common promoter: the maximum value was set as 0.4, because no obvious clusters were found for the analysis of promoter prediction. Then, if a binding site for one of four common transcription factors (nuclear respiratory factor 2 (NRF), GC boxes (GC), Yin and Yang 1 (YY), and activator protein 1 (AP)) was found, a value of 0.1 was subtracted. The columns "Expression profile cluster", "Amino acid encoding cluster", and "Synonymous codon frequency cluster" indicate the clusters to which RP genes were assigned as a result of each analysis. M: Main cluster; S1: Sub-cluster 1; S2: Sub-cluster 2; O: Other. The column "TATA box" indicates the existence of a TATA box, Y: Yes, N: No. For example, FI 3.3 of RPLP0 was calculated as follows; +1.0 (Expression profile), +1.0 (Amino acid encoding cluster), +0 (Synonymous codon frequency), +1.0 (TATA box), +0.4 -0.1 (Predicted Transcription Factors bound).