aminoacyl {ade4}R Documentation

Codon usage

Description

aminoacyl 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 charif@biomserv.univ-lyon1.fr starting from:
http://www.expasy.org/sprot/

References

Chiapello H., Olivier E., Landes-Devauchelle C., Nitschk√© 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$genes
aminoacyl$usage.codon
dudi.coa(aminoacyl$usage.codon, scannf = FALSE)

Worked out examples


> library(ade4)
> ### Name: aminoacyl
> ### Title: Codon usage
> ### Aliases: aminoacyl
> ### Keywords: datasets
> 
> ### ** 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 
> 
> 
> 
> 

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