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The basis of our analysis was the disease datasets, comprising of unique interactors of disease-gene products, which were manually verified as described before.
All mutations were manually verified as described in the Materials and Methods.
Novel candidate genes were manually verified as related to other known genes in nr, RefSeq and SwissProt databases using the web interfaces of Blast and PSI-blast [ 55].
The electrocardiographic wave complexes (QRS) were automatically classified and manually verified as normal sinus rhythm, arterial or ventricular premature beats, or noise by comparison of the adjacent QRS morphologic features.
Although a peptide tolerance of 3 Da was used in the search, the mass accuracy of the precursor ion scan for each identified peptide was manually verified as being within 20 ppm of the theoretical value.
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A database generated in a previous study [40] by surveying the scientific literature to find target-adverse effect associations and manually verified was used as a validation set (49 target-adverse effects).
All fragmentation spectra were manually verified using the criteria as described by Mann et al [48].
Peptide identification and peak-area integration of all targeted peptides as well as their transitions were manually verified in Pinpoint.
Peptide identification and peak-area integration of the GFP tag peptides and targeted synaptic peptides as well as their transitions were manually verified in Skyline.
Compared with the results of repetitive element prediction, LTR retrotranspons were further identified by LTR_finder software [ 42], and manually verified by structural features such as LTR and TSD pairs, a primer binding site and a polypurine tract.
This criterion differs from the various ways RRS was calculated in Guttman et al. principally in that RRS is additionally normalized for mRNA fragment density to control for transcript mis-annotation (Guttman et al., 2013), something we did not consider in our study as we manually verified the structures of all transcripts for which we report readthrough.
Related(20)
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