Codon usage
aminoacyl.Rdaminoacyl is a list containing the codon counts of 36 genes encoding yeast aminoacyl-tRNA-synthetase(S.Cerevisiae).
Usage
data(aminoacyl)Format
aminoacyl is a list containing the 5 following objects:
- genes
is a vector giving the gene names.
- localisation
is a vector giving the cellular localisation of the proteins (M = mitochondrial, C = cytoplasmic, I = indetermined, CI = cyto and mito).
- codon
is a vector containing the 64 triplets.
- AA
is a factor giving the amino acid names for each codon.
- usage.codon
is a dataframe containing the codon counts for each gene.
Source
Data prepared by D. Charif Delphine.Charif@versailles.inra.fr starting from:
http://www.expasy.org/sprot/
References
Chiapello H., Olivier E., Landes-Devauchelle C., Nitschké P. and Risler J.L (1999) Codon usage as a tool to predict the cellular localisation of eukariotic ribosomal proteins and aminoacyl-tRNA synthetases. Nucleic Acids Res., 27, 14, 2848--2851.
Examples
data(aminoacyl)
aminoacyl$genes
#> [1] "YCR024C" "YDR268W" "YGR094W" "YGR171C" "YHR011W" "YHR091C" "YKL194C"
#> [8] "YLR382C" "YNL073W" "YOL033W" "YPL040C" "YPL097W" "YPL104W" "YPR033C"
#> [15] "YPR047W" "YNL247W" "YPR081C" "YBL076C" "YBR121C" "YDR023W" "YDR037W"
#> [22] "YDR341C" "YER087W" "YFL022C" "YGL245W" "YGR185C" "YGR264C" "YHR019C"
#> [29] "YIL078W" "YLR060W" "YOL097C" "YOR335C" "YPL160W" "YHR020W" "YOR168W"
#> [36] "YLL018C"
aminoacyl$usage.codon
#> YCR024C YDR268W YGR094W YGR171C YHR011W YHR091C YKL194C YLR382C YNL073W
#> GCT 4 8 46 9 9 3 12 19 3
#> GCC 4 4 16 5 6 13 4 6 3
#> GCA 7 7 7 3 12 14 2 21 9
#> GCG 2 4 2 2 5 2 2 3 6
#> CGT 3 3 13 4 1 9 4 5 3
#> CGC 2 3 1 0 3 4 3 3 2
#> CGA 1 0 1 5 2 3 1 4 2
#> CGG 1 0 1 0 1 2 0 0 0
#> AGA 13 8 20 12 7 15 10 17 11
#> AGG 3 3 6 7 7 4 5 6 12
#> AAT 17 11 23 24 19 23 17 30 19
#> AAC 7 7 26 10 8 15 12 17 16
#> GAT 13 17 45 20 15 21 17 34 18
#> GAC 5 5 24 11 6 16 11 17 13
#> TGT 5 2 10 6 5 3 2 6 4
#> TGC 3 0 3 2 3 3 3 6 5
#> CAA 18 9 29 20 14 16 12 22 17
#> CAG 5 6 4 6 8 16 7 12 10
#> GAA 24 18 73 24 17 19 22 45 20
#> GAG 9 4 19 11 16 8 9 11 15
#> GGT 8 3 49 9 6 10 13 12 9
#> GGC 3 8 7 11 3 8 3 10 11
#> GGA 8 4 2 7 10 10 5 14 5
#> GGG 5 2 1 1 3 9 1 11 3
#> CAT 5 5 17 10 3 10 10 7 6
#> CAC 9 7 7 5 1 5 2 9 3
#> ATT 11 12 46 22 13 17 15 30 15
#> ATC 5 6 27 6 7 7 7 10 9
#> ATA 15 5 1 16 15 22 7 20 12
#> TTA 20 11 30 15 11 21 9 21 16
#> TTG 10 8 42 13 10 12 10 21 19
#> CTT 5 7 8 4 5 12 7 5 8
#> CTC 3 0 2 6 2 2 3 7 4
#> CTA 9 3 6 8 8 14 7 7 8
#> CTG 4 6 8 8 6 5 6 10 17
#> AAA 24 24 50 35 26 34 23 58 16
#> AAG 10 11 63 13 16 13 18 22 32
#> ATG 8 10 16 9 10 20 14 24 12
#> TTT 21 11 19 15 9 17 15 28 19
#> TTC 9 5 24 14 5 16 16 18 11
#> CCT 9 9 17 9 6 5 7 20 11
#> CCC 3 0 2 3 1 4 4 9 6
#> CCA 11 6 31 11 10 10 8 14 3
#> CCG 2 2 2 5 2 3 4 11 7
#> TCT 9 7 27 9 4 10 13 14 6
#> TCC 9 4 16 16 1 10 4 6 9
#> TCA 14 3 6 8 10 13 3 13 9
#> TCG 5 8 5 4 4 9 6 4 6
#> AGT 4 8 6 7 6 4 1 12 9
#> AGC 3 3 7 4 6 5 1 10 5
#> TAA 0 0 0 0 1 1 1 1 1
#> TAG 0 0 1 0 0 0 0 0 0
#> TGA 1 1 0 1 0 0 0 0 0
#> ACT 15 5 35 6 4 5 11 18 9
#> ACC 9 1 17 4 7 6 0 11 5
#> ACA 8 7 8 8 6 8 4 11 5
#> ACG 3 4 2 5 5 6 5 6 10
#> TGG 8 4 25 11 4 8 10 19 4
#> TAT 13 8 16 16 6 15 7 16 9
#> TAC 7 4 19 9 9 9 8 11 11
#> GTT 12 12 45 15 8 14 7 18 9
#> GTC 3 4 17 3 2 6 2 14 9
#> GTA 3 9 6 8 9 11 6 15 7
#> GTG 4 4 1 6 3 9 5 14 4
#> YOL033W YPL040C YPL097W YPL104W YPR033C YPR047W YNL247W YPR081C YBL076C
#> GCT 8 12 12 12 29 5 23 6 26
#> GCC 5 8 3 11 10 4 14 4 18
#> GCA 9 17 3 9 10 1 11 9 11
#> GCG 5 5 5 3 3 3 1 2 1
#> CGT 2 4 3 3 4 4 3 3 15
#> CGC 1 7 0 1 0 3 3 2 1
#> CGA 3 4 5 2 1 1 0 5 0
#> CGG 3 0 2 2 0 0 0 1 1
#> AGA 14 18 7 17 11 16 16 16 28
#> AGG 6 13 11 9 6 4 2 9 1
#> AAT 12 29 19 26 11 16 27 22 19
#> AAC 14 22 10 11 5 11 23 12 27
#> GAT 22 36 20 25 24 23 34 23 48
#> GAC 6 16 9 14 11 9 19 13 30
#> TGT 10 11 6 3 5 1 4 6 9
#> TGC 1 3 1 5 0 5 2 2 0
#> CAA 9 32 11 13 12 9 28 13 20
#> CAG 6 17 11 10 4 3 9 12 4
#> GAA 22 53 15 28 31 24 38 32 59
#> GAG 13 14 5 18 9 11 15 14 20
#> GGT 11 12 12 14 30 2 17 15 43
#> GGC 4 12 5 7 7 6 11 4 7
#> GGA 7 18 13 7 2 8 5 10 6
#> GGG 6 5 4 4 1 3 1 8 1
#> CAT 9 25 5 10 2 9 15 9 13
#> CAC 7 9 3 2 4 5 1 4 7
#> ATT 9 29 13 18 20 16 29 22 44
#> ATC 8 20 11 13 15 8 19 10 20
#> ATA 18 23 11 12 4 11 3 12 3
#> TTA 15 34 16 16 14 9 25 16 34
#> TTG 22 26 16 20 18 12 28 23 46
#> CTT 10 16 6 4 4 8 3 4 7
#> CTC 1 10 4 6 1 4 0 2 1
#> CTA 10 23 8 8 6 6 8 7 7
#> CTG 7 10 5 8 1 4 2 6 4
#> AAA 28 50 23 37 25 26 40 29 50
#> AAG 23 29 11 24 29 14 37 17 43
#> ATG 12 15 7 15 12 14 12 18 18
#> TTT 21 25 15 31 10 13 23 24 22
#> TTC 5 13 7 8 10 6 15 15 31
#> CCT 12 11 6 8 7 6 9 8 14
#> CCC 3 9 5 4 1 4 5 4 2
#> CCA 9 13 5 18 7 7 13 8 28
#> CCG 2 8 0 4 0 3 3 5 1
#> TCT 17 14 8 11 21 9 14 5 26
#> TCC 3 15 6 6 8 4 16 7 21
#> TCA 6 20 11 9 9 14 9 10 12
#> TCG 6 6 4 4 2 0 4 11 1
#> AGT 3 11 11 12 5 3 6 6 8
#> AGC 4 13 3 3 1 3 5 1 3
#> TAA 1 0 1 0 1 0 0 1 0
#> TAG 0 0 0 0 0 1 1 0 0
#> TGA 0 1 0 1 0 0 0 0 1
#> ACT 5 17 9 7 14 9 19 16 25
#> ACC 7 11 1 8 5 7 11 5 17
#> ACA 5 16 9 10 7 9 8 10 12
#> ACG 7 8 6 5 2 4 5 7 4
#> TGG 5 18 3 5 4 10 14 6 22
#> TAT 15 25 12 13 10 10 9 5 25
#> TAC 5 17 7 9 7 5 12 8 22
#> GTT 6 19 9 12 19 10 19 10 44
#> GTC 6 9 4 5 10 4 9 6 24
#> GTA 4 8 10 8 2 11 3 9 5
#> GTG 2 9 10 11 4 5 8 10 11
#> YBR121C YDR023W YDR037W YDR341C YER087W YFL022C YGL245W YGR185C YGR264C
#> GCT 25 16 21 18 10 10 35 11 22
#> GCC 17 6 14 10 3 12 13 9 11
#> GCA 7 1 1 11 6 4 3 6 13
#> GCG 0 1 1 4 5 1 1 5 1
#> CGT 5 4 9 7 4 4 10 0 10
#> CGC 2 0 1 1 2 0 0 0 1
#> CGA 0 0 0 0 3 0 0 0 0
#> CGG 0 0 0 0 1 0 0 0 0
#> AGA 26 12 23 19 12 15 23 8 12
#> AGG 3 1 2 1 6 0 3 2 1
#> AAT 13 11 10 13 24 9 15 9 30
#> AAC 10 12 11 13 11 17 21 12 24
#> GAT 29 17 24 22 31 15 43 10 30
#> GAC 20 7 17 12 10 20 21 8 15
#> TGT 6 5 8 2 11 1 6 3 10
#> TGC 0 3 1 1 4 0 1 1 0
#> CAA 15 17 24 20 11 20 16 15 24
#> CAG 1 4 2 4 11 5 0 2 3
#> GAA 52 40 46 36 27 26 44 23 44
#> GAG 9 11 9 14 10 12 2 7 7
#> GGT 30 21 29 28 14 21 24 17 29
#> GGC 5 2 2 7 8 2 6 4 2
#> GGA 4 3 1 3 11 1 6 1 5
#> GGG 2 0 1 0 3 4 1 1 1
#> CAT 12 5 7 7 8 4 4 3 17
#> CAC 3 4 9 7 5 8 10 2 5
#> ATT 21 12 17 22 13 9 28 9 23
#> ATC 14 13 10 18 11 17 18 12 15
#> ATA 2 1 1 1 14 1 4 0 3
#> TTA 18 17 12 24 17 7 19 10 22
#> TTG 32 17 27 18 15 23 32 19 34
#> CTT 3 2 5 6 5 9 1 4 4
#> CTC 0 1 1 1 2 4 1 2 1
#> CTA 2 4 5 6 6 7 7 5 8
#> CTG 1 0 2 6 11 8 1 1 6
#> AAA 30 24 23 29 35 20 27 21 34
#> AAG 30 26 25 22 15 21 49 21 28
#> ATG 12 6 20 19 16 14 17 9 10
#> TTT 22 7 13 15 18 7 8 12 18
#> TTC 11 13 17 14 5 19 21 8 14
#> CCT 7 3 7 5 6 8 8 6 9
#> CCC 0 1 0 3 4 4 2 2 1
#> CCA 23 15 23 11 9 8 20 17 24
#> CCG 0 0 3 1 1 0 0 1 0
#> TCT 19 12 11 15 5 11 13 5 22
#> TCC 11 10 7 5 4 12 6 5 7
#> TCA 4 3 3 5 14 3 5 3 10
#> TCG 0 0 1 3 6 4 1 1 5
#> AGT 5 3 0 1 11 0 2 3 7
#> AGC 0 1 1 2 5 1 3 2 3
#> TAA 1 1 1 1 0 1 1 1 1
#> TAG 0 0 0 0 1 0 0 0 0
#> TGA 0 0 0 0 0 0 0 0 0
#> ACT 13 7 12 11 8 5 20 5 11
#> ACC 9 4 10 5 4 16 13 8 2
#> ACA 4 1 7 8 8 6 2 2 12
#> ACG 2 1 0 1 2 3 2 2 7
#> TGG 7 6 2 9 10 6 12 1 13
#> TAT 10 8 7 13 8 3 8 7 20
#> TAC 8 13 13 11 10 12 15 6 15
#> GTT 33 15 15 24 10 9 22 14 32
#> GTC 17 8 14 8 7 12 22 8 7
#> GTA 1 4 3 3 6 0 1 1 1
#> GTG 0 1 1 2 4 3 6 3 6
#> YHR019C YIL078W YLR060W YOL097C YOR335C YPL160W YHR020W YOR168W YLL018C
#> GCT 20 17 16 6 39 43 25 20 21
#> GCC 12 17 16 7 19 24 17 7 14
#> GCA 9 3 3 7 8 24 7 15 8
#> GCG 0 2 2 2 2 6 0 6 0
#> CGT 9 10 7 4 12 15 5 3 10
#> CGC 1 0 0 1 1 1 2 0 1
#> CGA 0 0 0 0 0 0 0 0 0
#> CGG 0 0 0 0 0 0 0 0 0
#> AGA 17 27 17 10 20 20 26 14 19
#> AGG 0 2 1 1 2 5 3 5 6
#> AAT 4 12 14 7 27 18 13 15 4
#> AAC 8 20 18 4 23 21 10 12 12
#> GAT 11 30 22 20 49 50 29 16 10
#> GAC 26 14 18 15 24 14 20 9 23
#> TGT 8 9 8 5 6 11 6 7 3
#> TGC 1 3 1 1 1 2 0 2 0
#> CAA 20 23 15 19 23 31 15 14 18
#> CAG 4 4 3 3 3 6 1 1 5
#> GAA 34 56 31 22 66 81 52 29 43
#> GAG 10 8 16 6 12 18 9 8 14
#> GGT 27 31 18 17 60 42 30 17 27
#> GGC 6 5 6 4 10 9 5 3 1
#> GGA 3 6 0 2 3 3 4 13 0
#> GGG 1 5 4 2 3 6 2 3 4
#> CAT 8 13 7 7 11 12 12 9 4
#> CAC 2 6 8 2 5 8 3 5 8
#> ATT 13 21 20 11 29 46 21 24 16
#> ATC 14 13 19 6 24 22 14 11 12
#> ATA 1 1 4 2 3 6 2 9 0
#> TTA 7 21 15 7 20 28 18 13 6
#> TTG 35 31 25 16 38 30 32 21 36
#> CTT 1 1 5 3 8 5 3 8 3
#> CTC 2 0 0 0 1 1 0 1 2
#> CTA 5 6 8 4 6 9 2 9 7
#> CTG 4 3 2 3 6 4 1 4 2
#> AAA 13 32 23 18 39 47 30 24 16
#> AAG 30 33 23 26 52 53 30 15 32
#> ATG 11 22 13 8 10 27 12 16 11
#> TTT 7 18 13 16 26 30 22 10 12
#> TTC 15 21 16 19 27 29 11 5 16
#> CCT 3 4 7 7 11 19 7 11 7
#> CCC 2 0 0 1 4 1 0 3 5
#> CCA 17 22 21 12 22 29 23 15 14
#> CCG 0 2 2 1 1 3 0 3 0
#> TCT 13 28 11 3 25 28 19 16 7
#> TCC 13 7 13 9 11 6 11 9 10
#> TCA 3 3 5 4 8 12 4 6 2
#> TCG 1 2 4 2 1 2 0 1 1
#> AGT 2 6 2 1 3 3 5 5 5
#> AGC 3 1 3 5 2 5 0 2 3
#> TAA 0 1 1 1 1 1 1 1 0
#> TAG 0 0 0 0 0 0 0 0 0
#> TGA 1 0 0 0 0 0 0 0 1
#> ACT 12 18 9 9 26 23 13 9 5
#> ACC 17 10 14 10 13 15 9 4 13
#> ACA 5 2 4 6 8 13 4 12 6
#> ACG 2 0 3 2 1 6 2 6 1
#> TGG 4 13 4 3 8 13 7 1 1
#> TAT 10 8 4 3 13 26 10 9 6
#> TAC 13 16 13 9 22 26 8 7 12
#> GTT 13 24 17 12 36 25 33 18 11
#> GTC 15 18 12 8 16 17 17 11 11
#> GTA 4 3 6 5 3 8 1 10 4
#> GTG 3 1 4 7 6 3 0 10 7
dudi.coa(aminoacyl$usage.codon, scannf = FALSE)
#> Duality diagramm
#> class: coa dudi
#> $call: dudi.coa(df = aminoacyl$usage.codon, scannf = FALSE)
#>
#> $nf: 2 axis-components saved
#> $rank: 34
#> eigen values: 0.07774 0.01301 0.008387 0.007261 0.006383 ...
#> vector length mode content
#> 1 $cw 36 numeric column weights
#> 2 $lw 64 numeric row weights
#> 3 $eig 34 numeric eigen values
#>
#> data.frame nrow ncol content
#> 1 $tab 64 36 modified array
#> 2 $li 64 2 row coordinates
#> 3 $l1 64 2 row normed scores
#> 4 $co 36 2 column coordinates
#> 5 $c1 36 2 column normed scores
#> other elements: N