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Secondly, the SILAC test set consists of a larger number of proteins than considered in the other tests (see Table 2, SILAC test set Counts) and is most likely not biased towards proteins that are well annotated, as the much smaller literature datasets would be.
These ORFs are AYWB_379, PAM409, and PAM565, are annotated as " dam methylase", and the percentage identity is much lower, at 38% - 40%.
Interestingly, a much larger effect was observed in introns annotated as alternatively spliced, with 17.7% of these affected in prmt5 mutants and 17.8% in prmt4a 4b mutants.
Contigs were annotated as above.
Some names were crossed out with Vietnam dates; some were annotated as natural-cause eliminations.
Out of the 46 targets, 26 are annotated by the Census as oncogenes in the reported cancer type, 19 are annotated as tumour suppressors28, and one — CBL, encoding an E3 ubiquitin protein ligase — is annotated as having both functions.
As shown in Fig. 3B, 60% of them are classically annotated as secreted proteins.
TSSs located intergenic region without cognate gene were annotated as orphan (o).
Immune clusters for tumour regions without RNA-seq data are annotated as grey.
Similar observations can be made for all other genes annotated as having non-random RNA localization.
aWrongly annotated as pyruvate formate-lyase.bWrongly annotated as 3-dehydroquinate synthase.cWrongly annotated as 3-dehydroquinate synthase.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com