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Table 1 Sensitivity of the algorithms on the analysis of the influenza data

From: Identifying genetic determinants of complex phenotypes from whole genome sequence data

Site AB RRF Phenotype References
PB2 9 Infectivity [26]
PB2 105 Pathogenicity/Infectivity [27]
PB2 339 Infectivity [28, 29]
PB2 391   Transmissibility [30]
PB2 627 Infectivity [31]
PB2 667   Infectivity [32]
PB1 215 Pathogenicity [33]
PB1 375   Pathogenicity [34]
PB1 757   Infectivity [35]
HA 163   Pathogenicity/Infectivity [36]
HA 212   Pathogenicity/Infectivity [37]
HA 246 Transmissibility [38]
HA 536   Infectivity [39]
NP 400    Pathogenicity [40]
NA 49   Transmissibility [41]
NA 75    Transmissibility [42]
M2 31   Pathogenicity/Infectivity [41]
NS1 127    Pathogenicity [43]
NS1 195    Transmissibility/Infectivity [44]
NS1 212   Pathogenicity/Infectivity [45]
  1. This table lists the genes and amino acid positions known to be involved in the three phenotypes studied here, and which one of these were rediscovered by our algorithms. For AB, chunk sizes of 75, 125, and 175 were used to calculate the importance values of each site for adaptive boosting. An importance threshold of 1 was used to determine whether a site was a potential genetic determinant. For RRF, chunk sizes of 80, 125, and 175 were used with a threshold of the 90th percentile and a 60% consensus. Data on experimental validations are from the Influenza Research Database [24]. Genes are ordered by segment size. See Figs. 2 and 3 for the specificity of these algorithms