Most often genes classified by array analysis as absent were, in fact, expressed when measured by more sensitive RT-PCR methods, but were of very low abundance.
A typical bioinformatics example of this problem is finding co-regulated features, most often genes or, rather more precisely, their expression profiles.
More generally, we found, using the full STRING database, that those links which overlapped between CODA and any of the other fusion methods tended to have evidence from other types of prediction methods, most often gene neighbourhood.
Equally important and still challenging is the ability to deal with varying marker (most often gene) content: given reasonably divergent genomes, markers will have been variously lost or acquired over time.
Large subunits which possess the active site of Rubisco are encoded by the chloroplast gene rbcL, which over three decades ago was among the first fully sequenced genes [ 14] and since that time became one of the most often sequenced genes thanks to its wide use in phylogenetics of plants and algae (e.g. [ 15]).
As a consequence, rearrangements in mitochondrial genomes most often disrupt genes and thus are deleterious – a possible reason for the stability of mitochondrial gene order [ 4].
While promoter methylation is generally associated with lower transcription in A. thaliana [ 7], the relationship of gene body methylation to expression is complex, with methylation tending to occur most often in genes transcribed at moderate to high, but not very high, levels [ 4, 7, 8].
It is interesting to notice that the difference in the overlap clusters/TU concerns most often the genes located at the boundaries of the operons (see e.g. cl. 3, 5, 6, 10, and many more).
Most often, these genes are clustered in localized regions of the chromosome.
At present, the most often used genes to detect T. gondii are B1 and REP [ 7, 19, 38].
The VH1 gene distribution 17 months after therapy was largely comparable with that before treatment (i.e. VH1 18 and VH1 69 were the most often used genes).
