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Only miRNAs expressed in a minimum of 10 tumors and mapping to regions exhibiting loss or gain in a minimum of 5 tumors were included in our analysis.
Examples include inaccurate mapping due to sequencing errors, mapping to regions that are not transcribed but have homology to transcribed regions (for example to pseudogenes) and by missing small exons and/or introns to which isolated sort reads fail to map.
Using normalized expression topology, energy of binding, and the sum of sense and antisense smRNA reads mapping to regions of the hairpin other than mature miRNA or miRNA*, the SVM produced results nearly as predictive (81% versus 97%) as the Gold Standard training set of miRNA target genes (compare Tables 4 and 5).
Bases mapping to regions within a 500 bp range of a target were considered "near target".
To avoid analyzing nonorthologous introns, only introns mapping to regions of high-quality protein alignment were considered.
Although not mapping to regions with frequent genomic gains in the the included cases, previous reports have shown e.g. amplification of PRKCE on 2p21 [ 60] and FGF3 [ 61].
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The HA mutations tend to map to regions associated with receptor binding of the HA.
As expected, trajectories with a high risk map to regions of low expected feature.
To date, more than ten genes have been fine mapped to regions of less than 200 kb (Table 2).
Using these criteria, 97 miRNAs mapped to regions of aberrant copy number.
Both changes map to regions of unassigned functions within the HA protein.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com