Table 2.
Sites in our dataset modulated by any PDE inhibitor condition that are identified as regulatory in the PFP database (28)
Gene | Description | Amino acid | Position no. | Predictive models | RP | |||
B | L | M | R | |||||
LASP1 | LIM and SH3 domain protein 1 | S | 146 | — | — | — | — | + |
ARHGEF2 | Rho guanine nucleotide exchange factor 2 | S | 858 | — | — | + | — | + |
PTPN7 | Tyrosine-protein phosphatase nonreceptor type 7 | S | 125 | + | + | + | + | + |
BRAF | Serine/threonine-protein kinase B-raf | S | 446 | + | + | + | + | + |
NOP58 | Nucleolar protein 58 | S | 502 | — | — | — | — | + |
NUP50 | Nuclear pore complex prot Nup50 | S | 287 | — | — | — | — | + |
RAB3IP | Rab-3A-interacting protein | S | 162 | — | — | — | — | + |
BAD | Bcl2-associated agonist of cell death | S | 74/75 | + | — | — | + | + |
PGRMC1 | Member-associated progesterone receptor component 1 | S | 57 | — | — | — | — | + |
STAT1 | Signal transducer and activator of transcription | S | 727 | — | + | + | + | + |
SLC9A1 | Sodium/hydrogen exchanger 1 | S | 796 | — | — | — | + | + |
SP1 | Transcription factor Sp1 | S | 7 | + | + | + | + | + |
PRKCB | Protein kinase C β-type | S | 660 | — | + | + | — | + |
TBC1D1 | TBC1 domain family member 1 | T | 596 | + | + | + | + | + |
ETS1 | Protein C-ets-1 | S | 282 | + | — | + | + | + |
PPP1R2 | Protein phosphatase inhibitor 2 | S | 121 | + | + | + | + | + |
PPP1R2 | Protein phosphatase inhibitor 2 | S | 122 | + | + | + | + | + |
HMGA1 | High mobility group protein HMG-I/HMG-Y | T | 53 | — | — | — | — | + |
STMN1 | Stathmin | S | 63 | + | — | — | — | + |
CAD | CAD protein | S | 1,343 | + | + | + | + | + |
CAMKK1 | C++/calmodulin-dependent protein kinase kinase 1 | S | 485 | — | — | — | — | + |
USP20 | Ubiquitin carboxyl-terminal hydrolase 20 | S | 333 | — | — | — | — | + |
A truncated peptide sequence of four amino acid residues flanking the regulated phosphosite was used to screen the PFP proteomic database for predicted functional phosphosites. Predictive models used by PFP are Bayes (B), logistic (L), multilayer (M), and random (R). Empirically determined regulatory sites (RP) as derived from the PhosphositePlus database (29) are reported in the last column.