In addition, a formula function of two genes' discrepancies is fitted to the perceived dissimilarity between two car profiles.
Nevertheless, a common within-gene residual variance was assumed in these analyses, although within-gene discrepancies in the dispersion parameters could also be feasible.
Upon this, in a previous approach [ 26] we found that when LTR retroelement phylogenies are inferred from the concatenation of two or more protein domains, the statistical power of the analysis is increased and diverse (but not all) single-gene discrepancies are corrected.
Although on a global level, mRNA abundance correlates with the protein levels of the corresponding genes, discrepancies between mRNA and protein profiles have been noted for several genes in Streptomyces coelicolor [ 65].
Other gene expression discrepancies may also be due to cell proliferation and recruitment in bronchial mucosa as part of the pathogenesis of asthma.
Therefore, the procedure of including new annotation resources in aGEM will require a careful study, which will include ontology mapping and the resolution of gene nomenclature discrepancies.
For Drosophila cell-based RNAi screens, a library with three dsRNAs per gene, wherein discrepancies are disambiguated by requiring two of three dsRNAs to score, achieves a good balance between false negatives and false positives.
Here, the advantage of using the gag-pol alignment to infer the phylogeny is the increase in statistical power of the analysis, allowing the opportunity to correct the single gene tree discrepancies.
Their results support that highly expressed genes but probably not broadly expressed genes (see discrepancies between dataset 1 and 2) and certainly not genes with complex expression patterns have more compact introns and proteins.
Although the general topology among Flavobacteria, Sphingobacteria and Bacteroides branches was conserved with the three genes, several discrepancies could be detected between the 16S rRNA phylogeny and those of the other two genes (see black triangles and circles in Additional file 6 ).
