Figure 1.
Density plots for the raw PM probes intensity data.
The data are in log2 scale and the biological replicate arrays for rice varieties CP, LG and RT are shown in black, red and green color respectively. CP = Cypress, LG = LaGrue, RT = RT0034 and PM = perfect match.
Figure 2.
Pair-wise scatter plots for the raw PM probes intensity data across all arrays.
The intersection of 12000 randomly chosen features/probes data for CP and LG is boxed in blue, for CP and RT in red and for LG and RT in green respectively. The biological replicates of each variety are highly correlated as features are falling along diagonal line. CP = Cypress, LG = LaGrue, RT = RT0034 and PM = perfect match.
Table 1.
Number of gene-chip predicted SFPs called at different threshold (delta) in datasets.
Figure 3.
SAM plot of normalized data for CP&LG (a) and CP&RT (b) and LG&RT(c) pairs.
Observed d-statistics (y-axis) is plotted against the expected d-statistics (x-axis) as determined by permutations and SFPs exceeding the threshold are shown in green. The sign (+/−) with SFPs indicates direction of polymorphism. In (a) the (-) sign (i.e. CP-SFP) indicates polymorphism in LG (i.e. CP>LG) and (+) sign (i.e. LG-SFP) polymorphism in CP (i.e. LG>CP); in (b) the (-) sign (i.e. CP-SFP) signifies polymorphism in RT(i.e. CP>RT) and the (+) sign (i.e. RT-SFP) polymorphism in CP(i.e. RT>CP) and in (c) the (-) sign (i.e. LG-SFP) indicates polymorphism in RT (i.e. LG>RT) and (+) sign (i.e. RT-SFP) polymorphism in LG (i.e. RT>LG). CP = Cypress, LG = LaGrue and RT = RT0034.
Table 2.
Distribution of gene-chip predicted SFPs among polymorphic probesets.
Table 3.
Verification of gene-chip predicted SFPs by sequence information.
Table 4.
Nature of polymorphisms and detection sensitivity of SFPs.
Table 5.
Overlapping SFPs among gene-chip experiments datasets.
Table 6.
Overlapping SFPs between datasets of gene-chip experiments and in-silico analyses.
Figure 4.
Polymorphic features predicted by in-silico analyses and gene-chip experiments. NIP = Nipponbare; CP = Cypress; RT = RT0034 and PM = perfect match.