This is most likely to occur when doing gene set testing in systems biology, where specific gene sets have a length bias compared to other sets of genes.
We did not consider gene length as a variable in our multivariate analysis because gene length and fRNA coverage are not independent variables (due to the way the variable fRNA coverage is defined: see above).
This counting method was the most informative for this experiment and did not require gene length normalization.
The frequencies f1, f2, f3 have been derived from the set of codon samples of a gene and the normalization of frequency is done over the gene length in codons, in an attempt to compensate for the expected increase of RCB with the total number of codons.
As this resulted in a candidate pool of only 17 XR genes, and 36 autosomal genes, we did not further restrict this data set by gene length.
However, the number of exons predicts GC3 better than gene length does (supplementary table S1, Supplementary Material online).
Our analysis suggests that gene length does play a role in shaping the bias and shows strong correlation with the gene expression level.
Also, the proportion of AT->GC changes does not correlate with gene length anymore, indicating again the effect of gene position.
An intuitive order of genomes implied by the gene lengths is A, C, B. On the other hand, taking the genome average gene length does not agree with the intuitive order; it contradicts with the ordering of genomes (B, C) according to the gene b, and the ordering of the genomes (A, B) and (B, C) according to the gene c.
We therefore believe that the gene length does not have a major influence on the evolutionary rates of the genes analyzed here.> -wrap-foot> aGOI - gene of interest; HKG - housekeeping gene Esi0130_0068 was particularly interesting due to the presence of a REJ-like domain (IPR002859).
