Drugs with a Z score of <−1.7 in duplicate represent our positive candidates for this screen (p<0.002) and are in the lower left quadrants of Figure 2B C.
The microarrays contained a total of 668 probes spotted in duplicate, representing 328 known human miRNAs, 113 mouse miRNAs, 45 rat miRNAs, 154 predicted human miRNAs and 28 control probes (Ambion, Austin, TX, USA).
Interestingly, exon 6 in the PtGS1.1 duplicate represents the fusion of exons 6 and 7 in the PtGS1.2, PtGS1.3 and PtGS2 duplicates.
In total, the microarray consisted of 3623 PCR products spotted in duplicate representing every predicted open reading frame of the seven strains [ 8, 16].
An investigation of the gene locations of the NAC domain transcription factors in Populus trichocarpa showed that 6 pairs of NACs are present as tandem duplicates, represented in tandem clusters of 2 or 3 genes each.
On the other hand, the last exon in the PtGS1.1 and PtGS1.3 duplicates represents the fusion of exons 12 and 13 in the PtGS1.2 duplicate.
Gene duplicates represent 42% (7,327 genes) of the set of genes that where targeted at least once by an RNAi experiment.
Complete duplicates represent the most common structural category even when gene duplicates of varying evolutionary age were analyzed (cohorts K S = 0, 0 < K S ≤ 0.025, and 0.025 < K S ≤ 0.1).
Given the larger genome size and average gene length in humans relative to worm and Drosophila, it is paradoxical that complete duplicates represent the most abundant structural class of gene duplicates within the human genome.
Unequal crossing-over (nonallelic homologous recombination) between tandem gene duplicates represents a common mechanism for producing chimeric fusion genes in conjunction with changes in gene copy number (Holloway et al. 2006; Hoffmann et al. 2008b).
