Table I Comparison of SAM phosphosite output and experimental data
SAM output of differential phosphoregulationExperimental dataa
ΔNo. called significantNo. falsely significantFDR (SAM)No. regulated in Plk1as cellsNo. regulated in Plk1wt cells
2.1363960.00.0%3960
2.0114060.80.2%4060
1.8104420.80.2%4420
1.6094732.30.5%4721
1.4075093.90.8%5081
1.2065768.51.5%5751
1.00563517.82.8%6314
0.80478444.15.6%76713
0.6031214159.513.1%115254
0.4022765943.034.1%2432288
  • a For different Δ parameters, all phosphosites for which SAM reported significantly different ratios upon 3-MB-PP1 wash-out in Plk1as or in Plk1wt cells were analyzed whether their ratios deviated either in Plk1as or in Plk1wt cells more strongly from one.