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These genes are thought to be non-functional due to the presence of premature stop codon(s) interrupting the reading frame, and are currently not annotated as such by our automated annotation pipeline.
Other potential source of bias comes from the fact that only approximately 75% of all A. thaliana TFs have been used in our study, those that appear annotated as such in TAIR, thus we may be missing some relevant ones.
To mitigate the effect of ambiguous segmentation boundaries, we annotated the boundaries around the cracks as tightly as possible (making sure that only pixels completely contained inside the crack boundaries are annotated as such) and defined an envelope region around each crack whose labels are treated as 'do not care'.
Importantly, these genes have been described as epithelial genes in the literature, but heretofore have not been annotated as such in the GO ontology.
Over a thousand pseudogenes are now specifically annotated as such in WormBase [ 44].
In addition, proteins known to be members of a specific GH family were annotated as such.
This is only annotated as such in one instance in strain 26695, but not in the other three strains.
Another discrepancy was that some areas were detected as GIs that were not annotated as such in the genomes.
Many hypothetical proteins have been annotated as such because their sequence is found in open reading frames.
However, this was neither annotated as such, nor mentioned in the publication of McClain et al. [ 35].
Alternatively, they may identify sequences that are included in mature transcripts in T. castaneum but not annotated as such.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com