Table II Summary of log2 fold-change values for the 317 phosphopeptides that were detected in all three conditions of the signal-dependent phosphorylation experiment (supplemental Table S2 and Fig. 5)
A, abundance changes were coded as “up” or “down” if they changed by more than 1.34-fold (log2 ≥ 0.42), and each phosphopeptide was manually assigned to 1 of 27 possible patterns.
PatternCodeTemperaturepHpH + temperatureCount
1UUUUpUpUp20
2NUUUpUp20
3DUUDownUpUp2
4UNUUpUp25
5NNUUp56
6DNUDownUp4
7UDUUpDownUp2
8NDUDownUp13
9DDUDownDownUp1
10UUNUpUp4
11NUNUp8
12DUNDownUp0
13UNNUp16
14NNN85
15DNNDown10
16UDNUpDown4
17NDNDown24
18DDNDownDown11
19UUDUpUpDown0
20NUDUpDown1
21DUDDownUpDown0
22UNDUpDown0
23NNDDown3
24DNDDownDown3
25UDDUpDownDown0
26NDDDownDown4
27DDDDownDownDown1
Up7155143
No change214202162
Down326012
B, these patterns were used to ascribe a signal-dependent response to each phosphopeptide.
ResponseSignalPattern(s)Number of peptides
FullTemperature alone4 + 7 + 21 + 2430155
pH only2 + 3 + 25 + 2626
Temperature and pH1 + 2721
Temperature + pH5 + 6 + 8 + 9 + 19 + 20 + 22 + 2378
PartialTemperature only13 + 152677
pH only11 + 1732
Temperature and pH only10 + 12 + 16 + 1819
No changeNone148585