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The second junction (score = 1198) belongs to PF07_0101, a conserved Plasmodium protein of unknown function.
The first junction (score = 1300), in PFC0285c (predicted to encode the beta subunit of the class II chaperonin tailless complex polypeptide 1 ring complex), suggests an additional exon at the 5' end of the gene model, possibly belonging to the 5' untranslated region (UTR).
Each gene-specific transcript is then selected based on two independent criteria: (i) its status must be annotated as 'KNOWN' because we opted not to include 'novel' transcripts in our database as these are not yet validated by species-specific sequencing data (Bert Overduin from Ensembl Project, Personal communication) and (ii) the highest junction score.
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Consequently, alternative splicing is better visualized in the M-score plots where the constitutive junctions (the first five junctions plotted) score near zero, while the alternative junctions (last 6 or 7 junctions plotted) clearly score above and below the established cutoff (+/-1.3, gray dashed lines).
The average junction cleavage score for SBV decreased with increasing set sizes and was below the cleavage threshold even for small set sizes with an average score of −0.85 ± 1.09.
Survival comparisons are between patients with higher- or lower-than-average gene expression or tight junction index score, visualized via Kaplan-Meier analysis and assessed for significance via log-rank test.
For both methods, constitutively spliced junctions should score near zero while alternatively spliced junctions should have scores that differ substantially, either positively or negatively, from zero.
All phagosomes below the tight junction were scored as basal.
The average junction cleavage scores of SBVspacer and SBVAAY were stable and well above the cleavage threshold of 0.0 for all set sizes, with an average score of 1.74 ± 0.63 and 0.73 ± 0.53, respectively.
22 Four lid margin abnormalities (irregular lid margin, vascular engorgement, plugging of meibomian gland orifices and anterior or posterior replacement of the mucocutaneous junction) were scored from 0 through 4 according to the number of these abnormalities present in each eye.
The third and fourth junctions, with scores of 1261 and 1175, respectively, are in PFD0185c, another gene of unknown function conserved across Plasmodium species.
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