The enrichment analysis conducted by GeneCodis used pre-defined (>2 fold) DEGs as input, which exclude genes of minor fold changes that could be of biological significance in a given pathway.
The 605 pairs come from 272 duplicated gene pairs (which excluded genes that are part of a transposable element) from a recent duplication of rice chromosomes 11 and 12 (Fig. 1; A chromosomal alignment between chromosome 11 and 12 is provided in Additional file 1; a list of 272 duplicated gene pairs is provided as Additional file 2).
The apparent floor value of 0.10 to 0.25 for codon bias is consistent with a failure in our assumption that the set of test genes (which excludes core genes) is a random sampling of all native genes (including core genes) with respect to the measured quantity.
The Affymetrix array has probes for 32,101 of 38,869 non-TE genes, which excludes chloroplast, mitochondria and unmapped genes from the total non-TE genes, and 22,207 of 25,275 non-TE genes with FSTs were analyzed (Fig. 1).
Thus, an alternative approach to minimize the effects of fast evolving genes may rely on using a refined reference set which excludes fast evolving genes, such as Essien et al.'s method.
In the first filter, the 14,623 predicted coding genes of B. mori were compared with 382 genome sequences, which excluded 6,315 genes as possible HGT candidates since they have homologs only in insect genomes.
Deletion of large genomic regions has been observed in newly synthesized polyploids (Gaeta et al. 2007) so it might be argued that our analyses, which exclude all genes without identified homeologous regions, exclude a major category of fractionating gene loss.
Indeed, complete ethical assurance of somatic gene therapy can only be achieved with ultra-targeted gene delivery, which excludes the risk of inadvertent germline gene transfer.
Most plant T-DNA tagging vectors have so far been designed with the uidA (β-glucuronidase) reporter gene, which excludes non-destructive and real-time activity screening of the gene(s) tagged [ 8].
We therefore propose a "commercial wine strain signature" that comprises those genes whose copy number is altered in all the wine yeast isolates we examined relative to the sequenced S288C strain, but which excludes any of the genes whose copy numbers are altered in ale or beer strains or in other non-S288C laboratory strains such as SK1 and Y55.
