In the article by R. M. Kliman (G3: Genes|Genomes|Genetics 4: 681–692) entitled "Evidence that Natural Selection on Codon Usage in Drosophila pseudoobscura Varies Across Codons," Figure 5C and Figure 5D have been modified to correct an error in transcribing values during the production of the figure.
Based on our transcriptomic data, 264 of these hypothetical proteins were transcribed (FPKM values >0) in some D. immitis tissue (Additional file 10: Table S6).
Of the 1411 annotated features [ 1] in the Ap genome, 983 (69.6%) were significantly transcribed (p-value ≤ 0.05) in HL-60, 620 (43.9%) in HMEC-1, and 974 (69.0%) in ISE6, compared to negative control samples (RNA from uninfected cells).
These results suggest that roughly 50% of all genes are actively transcribed, a value similar to the typical percentage in other Drosophila tissues, based on mRNA seq [ 35] or array-based comparisons of germarium and testes [46% of all genes expressed; [ 36]].
Twelve of the 20 transcription errors were in the form of non-transcribed values.
When the values of SD sequence conservation were compared among the different ORFs, transcribed pseudogenes showed intermediate values between non-transcribed pseudogenes and functional ORFs (Fig. 7; also see Additional File 5 for specific ribosome-binding values for all M. leprae genes and pseudogenes).
DASE values of transcribed loci were calculated as described in the Methods section.
In this paper, we use an HMM to infer whether or not a segment of a strand of DNA is consecutively transcribed given the expression values obtained from the mapped reads.
To assign DASE value to transcribed loci, we used two approaches in parallel.
While the method detects around 40% of junction in genes transcribed above an RPKM value of 25.0, its detection rate decreases as RPKM further increases.
Using the average GEI for L. monocytogenes genes that were solely σB-dependent in the Δ sigB strain as a conservative cut-off value for transcribed genes, we found that approximately 83% of L. monocytogenes 10403S annotated CDS were transcribed in stationary phase cells.
