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ES values of various measurements in most annotated genes are also listed as an independent dataset.
Most annotated genes that do not form useful alignments are long and repetitive, with the majority being surface antigens.
Subsequent studies with improved mapping tools [ 2, 3] and increasingly deep sequencing depth [ 4, 5] suggested that, with enough depth of coverage, most annotated genes could be observed at some level.
Nevertheless, most annotated genes in N. vitripennis are in close proximity to a mapped marker; of the 10,734 genes in the N. vitripennis RefSeq gene set in Genbank, 94% are on a scaffold represented on the microarray, and those genes are on average 7.4 kb from the nearest marker.
In an attempt to capture multiple selection signals across the genome, selection-signal enrichment strength (ES) values of HET, F ST, and P-values of iHS of most annotated genes have been calculated and integrated within one frame for users to search for outliers.
The congruence of antisense tiling array signals to the exonic regions [14] manifest in antisense S/N ratios >>1 for most annotated genes (Supplemental Figure S3, Datafile S4) is remarkable and strongly suggests that the majority of antisense transcription occurs predominantly on spliced mRNAs and is dependent on the activity of RNA-dependent RNA polymerases.
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Although the microarray design encompassed most annotated gene models, the study was restricted to 1884 P. marneffei genes orthologous to S. cerevisiae genes with identified GO terms.
Manteia removes the multiplicity of annotation by assigning a single gene to a probeset by either removing the most poorly annotated genes or choosing one randomly when all are well annotated.
Using this method, we performed a comprehensive bioinformatic analysis that encompassed promoters of the 8110 most annotated human genes, 23,400 mouse genes and the known [35] PSSMs of 414 motifs M, using all functional GO groups to define the gene sets G that are scanned for enrichment.
Most of the annotated genes coded for proteins with homology to proteins in SwissProt18 (55.61%) and InterPro (ref. 19 65.5353%).
Most of the annotated genes expressed in any one species were detected in all three species (Additional file 3: Figure S2B).
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