Second, this makes our confirmation rate comparable with previous studies, such as Korbel et al. (2007), who suggested that events indicated by a single pair of reads may represent artifacts of the sample preparation, and therefore only confirmed events suggested by at least two data points; also see Doniger et al. (2008).
The data set was reduced as above to remove additional read-pairs mapping in the same location leaving 2,808 Class 2 events that were indicated by a single read-pair.
Of these events, 1,410 were indicated by a single uniquely mapping read-pair (table 2).
As shown in Figure 1, in the hairpin structure from RNAfold (Hofacker, 2003), each nucleotide in the sequence is either paired (indicated by a bracket, '(' or ')') or unpaired (denoted by a dot, '.').
Finally, there was a significantly stronger dependence between coexpression and function for gene pairs in the intersection network compared to the species-specific pairs as indicated by a comparison between expression profile correlations and GO functional similarity (Table 6).
It scores appropriate pairs of annotations, indicated by a relation, not individual annotations.
However, the association signal was not simply present on the high-risk haplotype TG (for rs6991170|rs6687758). Instead, the risks for the 'compound' (high-low or low-high) haplotypes GG and TA were greater than those for the low-low haplotype (GA), inconsistent with a functional SNP being in complete LD with a haplotype indicated by the pair of tagSNPs (Supplementary Material, Table S1).
Response specificity, as indicated by the paired difference indices calculated from within-block growth responses stimulated by the different Bradyrhizobium genotypes, differed significantly between host species and was more than three-fold greater in A. strigosus (mean PDI±1 1 S. E. = 6.6 ± 0.7) than in L. bicolor (mean PDI±1 1 S. E. = 1.7 ± 0.1).
A total of nine reciprocal coupling pairs with the strongest correlation between two residues were identified, as indicated by pair number (Figure 4c, Table 2).
This idea has led several groups to make the assumption that if a method identifies some structural covariation as indicated by contacting pairs, then other pairs with equivalent or higher scores not in contact must be caused by functional constraints [5], [8], [11].
