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. 2011 Mar 3;6(3):e17596. doi: 10.1371/journal.pone.0017596

Table 1. Direct comparison of expression levels of 50 wildtype and sequence-optimized human genes.

Ref_seq symbol PC length (bp) CAI % GC codons altered (n) codons altered (%) ratio expression expression statistics
wt opt wt opt wt: opt
NM_001514 TFIIB TF 948 0.77 0.97 44% 62% 213 67% 1∶1.18 +
NM_004379 CREB1 TF 981 0.76 0.96 47% 63% 213 65% 1∶2.80 +
NM_014596 ZNRD1 TF 409 0.83 0.98 54% 64% 69 55% 1∶3.41 +
NM_016269 Lef1 TF 1197 0.82 0.97 51% 63% 232 58% 1∶3.28 +
NM_006331 EMG1 RB 763 0.79 0.97 51% 64% 149 61% 1∶2.25 +
NM_139071 SMARCD1 RB 1305 0.82 0.98 52% 62% 248 57% 1∶1.85 +
NM_002648 PIM1 PK 939 0.85 0.97 59% 62% 137 44% 1∶1.12 +
NM_006875 PIM2 PK 933 0.82 0.97 60% 65% 167 54% 1∶1.28 +
NM_001001852 PIM3 PK 978 0.87 0.97 69% 66% 130 40% 1∶1.01  = 
NM_025195 Trb1 PK 1116 0.84 0.97 61% 64% 200 54% 1∶1.23 +
NM_004972 JAK2 PK 3396 0.77 0.98 39% 60% 784 69% 1∶6.00 +
NM_002110 HCK PK 1578 0.88 0.98 57% 62% 224 43% 1∶2.40 +
NM_005356 LCK PK 1527 0.87 0.98 58% 63% 222 44% 1∶1.90 +
NM_002019 FLT1 PK 4014 0.80 0.98 45% 60% 821 61% 1∶3.94 +
NM_002755 MAP2K1 PK 1179 0.84 0.97 53% 62% 207 53% 1∶1.05  = 
NM_004073 PLK3 PK 1938 0.84 0.97 61% 64% 322 50% 1∶1.15 +
NM_002745 Erk2 PK 1080 0.81 0.98 47% 61% 204 57% 1∶1.34 +
NM_001315 p38a PK 1080 0.82 0.98 47% 62% 213 59% 1∶2.57 +
NM_002750 JNK1 PK 1152 0.78 0.98 42% 60% 261 68% 1∶2.78 +
NM_002753 JNK3 PK 1266 0.81 0.98 45% 60% 238 56% 1∶14.73 +
NM_001292 CLK3 PK 487 0.85 0.97 60% 67% 92 61% 1∶0.97  = 
NM_001892 CK1a PK 1011 0.79 0.98 44% 60% 201 60% 1∶1.95 +
NM_003042 GAT1 MP 1797 0.87 0.98 56% 61% 254 42% 1∶1.19 +
NM_001045 Serotonin-TP* MP 1890 0.83 0.97 53% 60% 322 51% 1∶1.27 +
NM_030956 TLR10 MP 2433 0.76 0.98 38% 58% 551 68% only opt +
NM_014437 SLC39A1 MP 972 0.83 0.96 62% 65% 160 49% 1∶0.29 −
NM_000220 KCNJ1 MP 1173 0.81 0.98 45% 60% 231 59% only opt +
NM_001651 AQP5 MP 795 0.87 0.96 63% 63% 112 42% 1∶9.05 +
NM_001753 CAV1 MP 534 0.84 0.99 50% 59% 88 49% 1∶1.04  = 
NM_000593 TAP1 MP 2424 0.82 0.96 60% 65% 446 55% 1∶1.97 +
NM_000544 TAP2 MP 2109 0.84 0.96 59% 64% 345 49% 1∶2.37 +
NM_005561 LAMP1 MP 1251 0.84 0.97 56% 62% 206 49% 1∶1.28 +
NM_002294 LAMP2 MP 1230 0.78 0.98 43% 61% 280 68% only opt +
NM_014398 LAMP3 MP 1248 0.78 0.97 50% 64% 269 65% 1∶2.80 +
NM_000086 CLN3 MP 1314 0.84 0.97 60% 64% 211 48% 1∶2.64 +
NM_014319 LEMD3 MP 2733 0.76 0.96 52% 64% 583 64% 1∶1.29 +
NM_000914 OPRM1 MP 1200 0.83 0.98 49% 60% 212 53% 1∶2.70 +
NM_023921 TAS2R10 MP 921 0.75 0.99 36% 55% 204 66% only opt +
NM_024006 VKORC1 MP 520 0.83 0.98 59% 65% 73 45% 1∶0.76 −
NM_002507 NGFR MP 1281 0.88 0.97 66% 66% 170 40% 1∶1.15 +
NM_000585 IL-15 IM 486 0.73 0.98 36% 58% 126 78% only opt +
NM_011337.2 Mip1α IM 276 0.82 0.97 52% 59% 52 57% 1∶1.48 +
NM_000586 IL-2 IM 459 0.78 0.97 39% 58% 98 64% only opt +
NP_000610 IFNγ IM 498 0.77 0.98 39% 56% 116 69% 1∶1.81 +
NM_006850 IL-24 IM 618 0.82 0.98 50% 62% 103 50% 1∶1.20 +
NM_000572 IL-10 IM 534 0.86 0.98 51% 59% 80 45% 1∶1.35 +
NM_002985 RANTES IM 304 0.84 0.96 56% 62% 46 51% 1∶1.04  = 
NM_024013 IFNα IM 567 0.85 0.97 50% 61% 99 52% 1∶1.16 +
NM_001012271 BIRC5 other 495 0.84 0.96 54% 61% 84 51% 1∶4.24 +
NM_001786 CDC2 other 891 0.76 0.98 39% 59% 217 73% 1∶2.85 +

Columns left to right: Ref_seq.: Gene Bank accession number; symbol: encoded protein, e.g. *Serotonin-TP  =  Serotonin transporter; PC: protein class (TF  =  transcription factor; RB  =  ribosomal protein; PK  =  kinase; MP  =  membrane protein; IM  =  immunomodulator; and two other proteins); length: size of open reading frame in base pairs; CAI (codon adaptation index) [19], [48]: measure for the “relative adaptability” of the codon usage of the gene of interest to codons used in highly expressed genes. The CAI represents the geometric mean of the relative adaptiveness values of the used codons. The relative adaptiveness value of a synonymous codon represents the ratio of the frequency of this codon in the codon usage of a given expression system and the frequency of the most frequent synonymous codon for the specific amino acid, leading to a value of 1.0 for the optimal codon and less frequently used codons are scaled down accordingly. %GC: percentage of GC-content in the respective transgene; codons altered (n): total number of codons altered in the open reading frame; codons altered (%): percentage of codons altered in the open reading frame; ratio expression wt: opt: mean expression from three independent transfections of wildtype genes were set to 1 and then compared to the mean expression of optimized genes; expression statistics: wt<opt: +; wt = opt (+/− 10%):  = ; wt>opt: −. Average variations ≥10% were considered an improvement in expression (+).