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Genome-wide analysis of sequence divergence patterns in 12 024 human–mouse orthologous pairs reveals


Biology Articles » Biochemistry » Nucleic Acid Biochemistry » Reverse Polarization in Amino acid and Nucleotide Substitution Patterns Between Human–Mouse Orthologs of Two Compositional Extrema » Tables

Tables
- Reverse Polarization in Amino acid and Nucleotide Substitution Patterns Between Human–Mouse Orthologs of Two Compositional Extrema


Table 1. Amino Acid Replacement Matrix (AARM) for high-GC group in human mouse orthologs

Human
Gly Ala Arg Pro Phe Tyr Met Ile Asn Lys Ser Thr Cys Trp Val Leu Glu Asp His Gln
Mouse Gly 0.93 0.84 1.02 0.62 0.35 0.84 0.40 0.47 0.47 0.67 0.55 0.76 0.86 0.72 0.76 0.77 0.73 0.69 0.83
Ala 1.08 0.85 1.04 0.69 0.40 0.62 0.47 0.49 0.55 0.59 0.58 0.67 1.00 0.70 0.78 0.71 0.64 1.03 0.79
Arg 1.19 1.17 0.87 0.45 0.47 0.76 0.72 0.56 0.74 0.85 1.00 0.82 0.87 1.06 0.77 0.86 0.94 0.71 0.72
Pro 0.98 0.96 1.15 0.44 0.48 0.66 0.49 0.81 0.81 0.58 0.66 0.59 0.74 0.63 0.79 1.00 0.82 0.72 0.82
Phe 1.62 1.44 2.21 2.25 1.13 0.73 0.82 1.00 0.67 1.07 0.67 1.22 1.50 1.20 1.27 1.14 0.78 1.82 1.06
Tyr 2.82 2.50 2.12 2.09 0.88 1.00 0.85 1.13 1.71 1.31 1.53 1.25 1.33 0.70 1.08 1.83 1.68 1.50 1.61
Met 1.20 1.60 1.32 1.51 1.38 1.00 0.81 0.81 0.99 0.89 0.90 0.62 1.00 1.21 1.45 1.83 1.07 0.5 1.25
Ile 2.51 2.12 1.39 2.02 1.22 1.18 1.24 1.38 1.07 1.42 1.40 1.00 0.33 1.22 1.48 1.47 0.65 0.91 1.64
Asn 2.13 2.03 1.77 1.24 1.00 0.89 1.23 0.73 1.12 1.34 1.11 1.76 1.24 1.10 1.42 1.26 1.30 1.48
Lys 2.15 1.81 1.36 1.24 1.50 0.58 1.01 0.94 0.89 1.39 1.00 0.80 3.67 1.76 1.30 1.60 1.22 1.61 1.47
Ser 1.49 1.70 1.18 1.72 0.94 0.76 1.13 0.71 0.75 0.72 1.03 0.93 1.10 1.00 1.01 1.36 1.06 1.15 1.31
Thr 1.83 1.71 1.00 1.52 1.50 0.65 1.11 0.72 0.90 1.00 0.97 1.16 0.89 1.08 1.06 1.37 1.09 0.91 0.99
Cys 1.31 1.50 1.22 1.69 0.82 0.80 1.60 1.00 0.57 1.25 1.07 0.86 1.17 1.04 0.98 0.75 1.17 1.01 0.63
Trp 1.16 1.00 1.15 1.35 0.67 0.75 1.00 3.00 0.27 0.91 1.12 0.85 1.05 0.94 1.00 0.33 0.59 0.76
Val 1.40 1.43 0.94 1.60 0.84 1.43 0.82 0.82 0.8 0.57 1.00 0.93 0.96 0.95 1.08 0.81 0.86 1.17 1.07
Leu 1.31 1.28 1.31 1.26 0.79 0.92 0.69 0.67 0.91 0.77 0.99 0.94 1.02 1.07 0.92 1.51 1.04 1.16 0.88
Glu 1.30 1.41 1.16 1.00 0.88 0.55 0.55 0.68 0.71 0.62 0.74 0.73 1.33 1.00 1.23 0.66 0.85 0.79 0.86
Asp 1.38 1.57 1.06 1.22 1.29 0.59 0.93 1.53 0.80 0.82 0.95 0.92 0.86 3.00 1.16 0.96 1.17 0.94 1.26
His 1.45 0.97 1.41 1.38 0.55 0.67 2.00 1.10 0.77 0.62 0.87 1.10 0.99 1.70 0.85 0.86 1.27 1.06 1.02
Gln 1.20 1.27 1.38 1.21 0.94 0.62 0.80 0.61 0.68 0.68 0.76 1.01 1.58 1.31 0.93 1.13 1.17 0.79 0.98

Each element Rij in the AARM represents the ratio of number of replacements of the residue i by the residue j in the forward direction (mouse -> human) to that in the reverse direction. This means that if Rij >1, the number of (i)Mouse-> (j)Human replacements is higher than the number of (j)Mouse-> (i)Human replacements and if Rij p



Table 2. Amino Acid Replacement Matrix (AARM) for medium-GC group in human mouse orthologs

Human
Gly Ala Arg Pro Phe Tyr Met Ile Asn Lys Ser Thr Cys Trp Val Leu Glu Asp His Gln
Mouse Gly 0.92 0.90 1.09 0.93 0.9 1.04 0.76 0.84 0.83 0.92 0.73 0.89 0.90 1.10 1.20 0.97 0.88 0.69 0.80
Ala 1.09 1.19 1.08 1.19 1.00 0.9 0.85 0.97 1.05 0.85 0.85 0.8 0.59 0.95 0.96 0.90 0.74 1.06 1.21
Arg 1.11 0.84 1.02 0.91 0.84 0.85 0.76 1.04 1.09 1.10 1.07 1.07 1.23 0.91 0.92 1.12 0.98 0.95 0.89
Pro 0.92 0.93 0.98 0.76 0.61 1.21 0.82 0.79 1.03 0.82 0.97 0.62 1.75 0.77 0.85 1.05 0.78 1.11 1.15
Phe 1.08 0.84 1.10 1.32 1.19 0.72 0.95 1.41 1.67 0.98 0.93 0.97 1.38 0.82 1.01 1.80 0.93 1.62 1.15
Tyr 1.11 1.00 1.19 1.64 0.84 1.25 0.78 0.88 0.94 0.94 1.12 0.91 1.32 1.04 0.84 1.12 0.86 1.12 0.88
Met 0.97 1.11 1.17 0.82 1.38 0.80 1.09 0.96 0.86 0.77 0.86 1.11 0.75 0.98 1.11 0.91 0.65 0.93 1.46
Ile 1.32 1.18 1.32 1.21 1.05 1.29 0.92 1.13 1.02 1.03 0.95 1.28 0.25 0.85 0.92 1.33 0.88 0.83 1.29
Asn 1.19 1.04 0.96 1.27 0.71 1.13 1.04 0.88 1.00 0.89 0.88 0.76 1.33 0.89 0.92 1.07 1.01 0.98 0.72
Lys 1.20 0.95 0.92 0.97 0.60 1.06 1.16 0.98 1.00 0.89 0.84 0.73 1.94 1.05 1.35 1.13 0.87 0.81 1.04
Ser 1.09 1.18 0.91 1.22 1.02 1.06 1.30 0.97 1.13 1.13 1.17 0.91 1.10 1.08 1.05 1.14 1.04 1.05 1.22
Thr 1.38 1.17 0.93 1.03 1.08 0.89 1.16 1.06 1.14 1.20 0.85 0.86 0.57 1.06 0.80 1.05 0.93 0.80 1.15
Cys 1.12 1.24 0.93 1.62 1.03 1.10 0.90 0.78 1.31 1.36 1.09 1.16 0.93 0.84 1.18 1.00 0.76 0.93 1.00
Trp 1.11 1.70 0.81 0.57 0.72 0.76 1.33 4.00 0.75 0.52 0.91 1.75 1.08 1.30 0.89 0.76 0.75 0.55 0.83
Val 0.91 1.06 1.10 1.30 1.21 0.96 1.02 1.17 1.12 0.96 0.92 0.94 1.19 0.77 1.05 0.91 0.72 0.90 1.02
Leu 0.83 1.04 1.08 1.18 0.99 1.19 0.90 1.09 1.09 0.74 0.95 1.25 0.84 1.12 0.95 0.98 1.39 1.10 0.94
Glu 1.03 1.11 0.89 0.95 0.56 0.89 1.10 0.75 0.93 0.88 0.87 0.95 1.00 1.32 1.10 1.02 0.86 0.69 0.91
Asp 1.14 1.35 1.03 1.29 1.07 1.17 1.55 1.14 0.99 1.15 0.96 1.08 1.32 1.33 1.38 0.72 1.16 0.81 0.83
His 1.45 0.95 1.06 0.90 0.62 0.90 1.08 1.20 1.02 1.23 0.95 1.25 1.07 1.83 1.11 0.91 1.46 1.23 1.06
Gln 1.25 0.83 1.13 0.87 0.87 1.13 0.69 0.78 1.38 0.96 0.82 0.87 1.00 1.21 0.98 1.06 1.09 1.21 0.94

Each element Rij in the AARM represents the ratio of number of replacements of the residue i by the residue j in the forward direction (mouse -> human) to that in the reverse direction. This means that if Rij >1, the number of (i)Mouse-> (j)Human replacements is higher than the number of (j)Mouse-> (i)Human replacements and if Rij p



Table 3. Amino Acid Replacement Matrix (AARM) for low-GC group in human mouse orthologs

Human
Gly Ala Arg Pro Phe Tyr Met Ile Asn Lys Ser Thr Cys Trp Val Leu Glu Asp His Gln
Mouse Gly 0.88 0.98 0.91 2.10 1.50 1.60 2.08 1.77 1.22 1.15 1.09 1.32 0.97 1.80 1.56 1.29 1.35 1.23 1.08
Ala 1.13 0.97 1.24 1.61 1.32 1.36 1.67 1.97 1.97 1.24 1.25 0.97 3.00 1.28 1.37 1.31 1.24 1.62 1.45
Arg 1.02 1.03 0.97 1.32 1.38 1.45 1.50 1.89 1.63 1.18 1.14 1.11 0.97 1.04 1.23 1.40 1.69 1.41 1.09
Pro 1.10 0.81 1.03 1.34 2.43 1.40 1.64 2.63 2.00 1.26 1.51 0.77 1.07 1.10 1.15 1.45 1.32 1.56 1.69
Phe 0.48 0.62 0.76 0.74 1.25 0.68 0.95 1.21 1.54 0.76 0.75 0.60 0.68 0.64 0.78 0.76 0.50 0.92 0.85
Tyr 0.67 0.76 0.72 0.41 0.80 0.73 1.12 0.86 0.93 0.67 0.70 0.74 1.38 0.76 0.91 1.00 0.80 0.77 0.83
Met 0.62 0.73 0.69 0.71 1.46 1.38 1.48 1.23 1.05 0.83 0.88 0.50 0.38 0.81 0.84 0.60 0.96 0.87 1.04
Ile 0.48 0.60 0.67 0.61 1.05 0.89 0.68 1.17 1.00 0.65 0.66 0.50 0.89 0.67 0.68 0.65 0.70 0.96 0.57
Asn 0.57 0.51 0.53 0.38 0.83 1.16 0.81 0.86 1.04 0.57 0.60 0.54 0.14 0.72 0.68 0.90 0.81 0.57 0.74
Lys 0.82 0.51 0.61 0.50 0.65 1.08 0.95 1.00 0.96 0.62 0.62 0.75 0.65 0.77 0.70 0.93 0.89 0.57 0.73
Ser 0.87 0.80 0.85 0.79 1.32 1.48 1.20 1.53 1.74 1.60 1.26 0.76 0.66 1.04 1.15 1.33 1.39 0.99 1.10
Thr 0.91 0.80 0.88 0.66 1.33 1.43 1.13 1.51 1.67 1.60 0.79 1.00 1.8 0.91 0.91 1.19 1.08 0.91 1.05
Cys 0.76 1.03 0.90 1.30 1.67 1.36 2.00 2.00 1.84 1.33 1.31 1.00 1.00 0.52 1.11 0.57 1.44 0.94 1.31
Trp 1.03 0.33 1.03 0.93 1.48 0.73 2.67 1.12 7.00 1.54 1.52 0.56 1.00 1.22 1.16 1.19 0.8 0.94 1.11
Val 0.55 0.78 0.96 0.91 1.56 1.32 1.23 1.48 1.39 1.31 0.96 1.10 1.91 0.82 1.13 0.79 0.89 1.16 0.97
Leu 0.64 0.73 0.82 0.87 1.28 1.09 1.19 1.48 1.47 1.42 0.87 1.09 0.9 0.86 0.89 0.92 0.58 1.13 0.92
Glu 0.78 0.76 0.71 0.69 1.31 1.00 1.67 1.53 1.12 1.08 0.75 0.84 1.75 0.84 1.27 1.09 0.84 1.06 0.95
Asp 0.74 0.81 0.59 0.76 2.00 1.25 1.04 1.43 1.24 1.12 0.72 0.93 0.69 1.25 1.12 1.72 1.19 0.78 1.00
His 0.81 0.62 0.71 0.64 1.09 1.30 1.15 1.04 1.76 1.75 1.01 1.10 1.07 1.06 0.86 0.89 0.94 1.28 1.09
Gln 0.93 0.69 0.92 0.59 1.170 1.20 0.96 1.77 1.36 1.37 0.91 0.95 0.77 0.90 1.03 1.08 1.05 1.00 0.91

Each element Rij in the AARM represents the ratio of number of replacements of the residue i by the residue j in the forward direction (mouse -> human) to that in the reverse direction. This means that if Rij >1, the number of (i)Mouse-> (j)Human replacements is higher than the number of (j)Mouse-> (i)Human replacements and if Rij p



Table 4. Top 15 amino acid pairs of three orthologous groups according to differences in number of forward (mouse to human) and reverse (human to mouse) replacements in AARM

Pair Forward no. Reverse no. Difference Ratio Codon changes Trends
High-GC group
Thr -> Ala* 6873 4020 2853 1.71 ACN -> GCN ±
Ser -> Ala* 4160 2447 1713 1.70 UCN/AGY -> GCN ±
Ser -> Pro* 3603 2097 1506 1.72 UCN/AGY -> CCN ±
Val -> Ala* 4484 3144 1340 1.43 GUN -> GCN ±
Ser -> Gly* 3749 2516 1233 1.49 UCN/AGY -> GGN +
Gln -> Arg* 3389 2448 941 1.38 CAR -> CGN/AGR
Lys -> Arg* 3412 2518 894 1.36 AAR -> CGN/AGR ±
Ile -> Val* 4572 3756 816 1.22 AUH -> GUN ±
Asn -> Ser* 2878 2145 733 1.34 AAY -> UCN/AGY ±
Asp -> Glu* 3799 3237 562 1.17 GAY -> GAR
His -> Arg* 1899 1343 556 1.41 CAY -> CGN/AGR +
Met -> Leu* 1753 1211 542 1.45 AUG -> UUR/CUN +
Ile -> Leu* 1500 1012 488 1.48 AUN -> UUR/CUN ±
Lys -> Glu* 1257 785 472 1.60 AAR -> GAR
Leu -> Pro* 2060 1634 426 1.26 YYR/CUN -> CCN +
Medium-GC group
Val -> Ile* 5839 4982 857 1.17 GUN -> AUH {square}
Thr -> Ala* 5566 4753 813 1.17 ACN -> GCN {circ}
Ser -> Pro* 3804 3113 691 1.22 UCN/AGY -> CCN {circ}
Asp -> Glu* 4443 3833 610 1.16 GAY -> GAR
Ser -> Thr* 3652 3113 539 1.17 UCN/AGY -> ACN {square}
Ser -> Ala* 3507 2972 535 1.18 UCN/AGY -> GCN {circ}
Ser -> Asn* 3626 3213 413 1.13 UCN/AGY -> AAY {square}
Arg -> Lys** 4017 3701 316 1.08 CGN/AGR -> AAR {square}
Leu -> Pro* 1999 1691 308 1.18 UUR/CUN -> CCN {circ}
Gln -> Arg* 2676 2372 304 1.13 CAR -> CGN/AGR {circ}
Ser -> Gly 2782 2560 222 1.09 UCN/AGY -> GGN {circ}
Val -> Ala 3759 3561 198 1.06 GUN -> GCN {circ}
Lys -> Glu** 1514 1336 178 1.13 AAR -> GAR {circ}
Asp -> Ala* 661 488 173 1.35 GSN -> GCN
Met -> Leu 1648 1483 165 1.11 AUG -> UUR/CUN {circ}
Low GC group
Val -> Ile* 9402 6335 3067 1.48 GUN -> AUH ±
Ser -> Asn* 6508 3733 2775 1.74 UCN/AGY -> AAY ±
Arg -> Lys* 6603 4059 2544 1.63 CGN/AGR -> AAR ±
Ala -> Thr* 6393 5117 1276 1.25 GCN -> ACN ±
Leu -> Ile* 3003 2035 968 1.48 UUR/CUN -> AUH ±
Asp -> Glu* 5952 5014 938 1.19 GAY -> GAR
Ser -> Thr* 4498 3563 935 1.26 UCN/AGY -> ACN
Ala -> Val* 4193 3264 929 1.28 GCN -> GUN ±
Thr -> Ile* 2612 1733 879 1.51 CAN -> AUH
Pro -> Ser* 4178 3304 874 1.26 CCN -> UCN/AGY ±
Ala -> Ser* 3975 3195 780 1.24 GCN -> UCN/AGY ±
Leu -> Phe* 2990 2330 660 1.28 UUR/CUN -> UUY
Thr -> Asn* 1630 975 655 1.67 CAN -> AAY
Met -> Ile* 1900 1288 612 1.48 AUG -> AUH
His -> Asn* 1258 715 543 1.76 CAY -> AAY

*,**Replacements of pairs are significant at p

Symbols used in codons: R, A/G; Y, C/T; S, G/C; W, A/T; H, A/C/T; N, any nucleotide. Symbols used in trends: opposite trends among top 15 amino acid pairs of both high- and low-GC groups (±); opposite trends in high- and low-GC group, but not present in top 15 of low-GC group (+); opposite trends in high- and low-GC group, but not present in top 15 of high-GC group (–); same trend in high-, medium-, and low-GC groups (•); same trend in high- and medium-GC groups ({circ}); same trend in low- and medium-GC groups ({square}).



Table 5. Nucleotide replacement matrices at (NRMs) three codon positions for human mouse orthologs of high-, medium-, and low-GC groups under study

Human
Group First codon position
Second codon position
Third codon position
Mouse A T G C A T G C A T G C
High-GC group A - 1.00 1.13 1.16 - 1.01 1.08 1.06 - 1.00 1.86 1.71
T 1.00 - 1.11 1.19 0.99 - 1.06 1.06 1.00 - 1.69 1.86
G 0.88 0.90 - 1.01 0.92 0.95 - 0.98 0.54 0.59 - 1.01
C 0.86 0.84 0.99 - 0.94 0.95 1.02 - 0.58 0.54 0.99 -
Medium-GC group A - 1.01 1.02 1.03 - 0.99 1.01 1.01 - 1.00 1.04 1.01
T 0.99 - 1.03 1.02 1.01 - 1.02 1.02 1.00 - 1.02 1.03
G 0.98 0.97 - 1.00 0.99 0.98 - 1.00 0.97 0.98 - 1.00
C 0.97 0.98 1.00 - 0.99 0.98 1.00 - 0.99 0.97 1.00 -
Low-GC group A - 1.01 0.93 0.90 - 0.99 0.90 0.94 - 0.99 0.64 0.65
T 0.99 - 0.93 0.83 1.01 - 0.94 0.95 1.01 - 0.70 0.62
G 1.08 1.07 - 0.97 1.11 1.06 - 1.02 1.56 1.42 - 0.96
C 1.11 1.20 1.03 - 1.07 1.06 0.98 - 1.53 1.62 1.04 -

Each element rij in the NRM represents the ratio of number of replacements of the nucleotide i by the nucleotide j in the forward direction (mouse to human) to that in the reverse direction. This means that if rij > 1, the number of (i)Mouse-> (j)Human replacements is higher than the number of (j)Mouse-> (i)Human replacements and if rij p



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