How to choose the cut-off values and the thresholds?
Firstly, we calculated the theoretically maximal false positive rate (FPR) for each PK cluster. The three thresholds of GPS 2.1 were decided based on calculated FPRs.For serine/threonine kinases, the high, medium and low thresholds were established with FPRs of 2%, 6% and 10%. And for tyrosine kinases, the high, medium and low thresholds were selected with FPRs of 4%, 9% and 15%. The high threshold was validated by a large-scale prediction of mammalian phosphorylation sites, with a satisfying performance. And the medium threshold relaxed the stringency to be useful in small-scale experiments. Also, the low threshold reduced the Sp to improve Sn considerably to be useful in exhaustively experimental identifying all potential phosphorylation sites in substrates.
