Codon Bias
Codon bias data is calculated by the method of Bennetzen and Hall (1982) . The maximum value of codon bias (CB) is 1.0, and the minimum value can be negative. Higher valulue can be negative. Higher values indicate greater degree of gene expression.
Bennetzen, J.L. & Hall, B.D. Codon selection in yeast. J. Biol. Chem. 1982 Mar 25;257(6):3026-31

Codon Adaptation Index
Codon adaptation index is calculated by the method of Sharp and Li (1987). The maximum value of codon adaptation index is 1.0 and the minimum value is 0. Highly expressed proteins have CAI greater than 0.500, moderately expressed proteins have CAI values between 0.200 and 0.500, poorly expressed proteins have CAI values between 0.100 and 0.200, while CAI values below 0.100 generally mean that the protein is expressed below detectable amounts, if expressed at all.
Sharp, P.M. & Li, W.H. The Codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987 Feb 11;15(3):1281-95.

How to search the dataset?
 You can search for a string in the name column or in the ORF column. The program will look for any record containing this string. For exemple, if you submit the query "gene containing: dr", you will obtain DRS2, PDR3, ADR1, PDR15, PDR1, ...
Some tips:
    - the search is case insensitive
    - the ratios are shown visually by the classical color code: red = hight MLR, green = low MLR.

Karlberg paper
Archea
Bacteria
C. elegans
R. prowazetti
R. americana Mitochondrion
only Eucaryotic homologs
unique to Yeast

The dual origin of the yeast mitochondrial proteome.
Karlberg O, Canback B, Kurland CG, Andersson SG
Yeast 2000 Sep 30;17(3):170-187
Karlberg's paper homepage

abstract of Karlberg's paper:
We propose a scheme for the origin of mitochondria based on phylogenetic reconstructions with more than 400 yeast nuclear genes that encode mitochondrial proteins. Half of the yeast mitochondrial proteins have no discernable bacterial homologues, while one-tenth are unequivocally of alpha-proteobacterial origin. These data suggest that the majority of genes encoding yeast mitochondrial proteins are descendants of two different genomic lineages that have evolved in different modes. First, the ancestral free-living alpha-proteobacterium evolved into an endosymbiont of an anaerobic host. Most of the ancestral bacterial genes were lost, but a small fraction of genes supporting bioenergetic and translational processes were retained and eventually transferred to what became the host nuclear genome. In a second, parallel mode, a larger number of novel mitochondrial genes were recruited from the nuclear genome to complement the remaining genes from the bacterial ancestor. These eukaryotic genes, which are primarily involved in transport and regulatory functions, transformed the endosymbiont into an ATP-exporting organelle. Copyright 2000 John Wiley & Sons, Ltd.

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Where can I find descriptions of the experiments?
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If you still have a question that is not answered here please email to Pr. Claude Jacq.