Table 6. Overlapping SFPs between datasets of gene-chip experiments and in-silico analyses.
| (a) CP&LG vs. Nip&93-11 | (b) CP&RT vs. Nip&93-11 | ||||||||
| Nip&93-11(in-silico) | Nip&93-11(in-silico) | ||||||||
| −SFP | non-SFP | +SFP | −SFP | non-SFP | +SFP | ||||
| CP&LG(gene-chip) | 64774 | 316896 | 3328 | CP&RT(gene-chip) | 64774 | 316896 | 3328 | ||
| −SFP | 3615 | 1638 | 1908 | 69 | −SFP | 28296 | 17041 | 11113 | 142 |
| non-SFP | 379530 | 62277 | 314077 | 3176 | non-SFP | 347932 | 46144 | 299323 | 2465 |
| +SFP | 1853 | 859 | 911 | 83 | +SFP | 8770 | 1589 | 6460 | 721 |
| Chi-sq. = 3711.629, df = 4, p-value<2.2e-16 | Chi-sq. = 46973.71, df = 4, p-value<2.2e-16 | ||||||||
| (c) LG&RT vs. Nip&93-11 | (d) Common of common SFPs of (b) & (c) | ||||||||
| Nip&93-11(in-silico) | (c) | ||||||||
| −SFP | non-SFP | +SFP | −SFP | +SFP | |||||
| LG&RT(gene-chip) | 64774 | 316896 | 3328 | (b) | 17699 | 844 | |||
| −SFP | 29369 | 17669 | 11545 | 155 | −SFP | 17401 | 14817 | 0 | |
| non-SFP | 343875 | 45012 | 296534 | 2329 | +SFP | 721 | 0 | 627 | |
| +SFP | 11754 | 2093 | 8817 | 844 | |||||
| Chi-sq. = 48561.51, df = 4, p-value<2.2e-16 | |||||||||
The gene-chip predicted SFPs data for CP&LG, CP&RT and LG&RT have been taken from estimated FDR (delta) of 11.9% (delta = 2), 10% (delta = 2)and 10% (delta = 1.6) respectively. The SFP data for Nip&93-11 have been taken from in-silico analyses(see methods; supplementary Table S3). The table has been generated from 384998 features shared by gene-chip and in-silico analyses. The sign(+/−) indicates direction of polymorphism as explained in Figure-3 and Table S3 legend. CP = Cypress, LG = LaGrue, RT = RT0034 and Nip = Nipponbare.