Table 1.
Comparing Sites Observed in FL-HCC Tissue (Higher in Tumor vs Adjacent Normal; Turnham et al., eLife, 2019)11 and the HEK293 J-PKAca and/or WT PKAca Overexpression Models
| all three | ||||||
|---|---|---|---|---|---|---|
|
| ||||||
| uniprot ID | gene name | entry name | protein name | site | sequence | directa |
| P12956 | XRCC6 | XRCC6_HUMAN | X-ray repair cross-complementing protein 6 (Ku70) | 520 | AMNKRLGSLVDEFKE | xxxx |
| P39023 | RPL3 | RL3_HUMAN | 60S ribosomal protein L3 | 13 | FSAPRHGSLGFLPRK | xxxx |
| Q02790 | FKBP4 | FKBP4_HUMAN | peptidyl-prolyl cis-trans isomerase FKBP4 | 78 | LDRKDKFSFDLGKGE | xx |
| Q08211 | DHX9 | DHX9_HUMAN | ATP-dependent RNA helicase A (DEAH box protein 9) | 449 | VTQPRRISAVSVAER | xx |
| Q04917 | YWHAH | 1433F_HUMAN | 14–3-3 protein eta (protein AS1) | 145 | ASGEKKNSVVEASEA | xx |
| Q14690 | PDCD11 | RRP5_HUMAN | protein RRP5 homologue (NF-kappa-B-binding protein) | 926 | ARKLRKGSEHQAIVQ | x |
| P11940 | PABPC1 | PABP1_HUMAN | polyadenylate-binding protein 1 (PABP-1) | 96 | RDPSLRKSGVGNIFI | x |
| P48147 | PREP | PPCE_HUMAN | prolyl endopeptidase (PE) | 667 | VGRSRKQSNPLLIHV | x |
| P62888 | RPL30 | RL30_HUMAN | 60S ribosomal protein L30 | 10 | AAKKTKKSLESINSR | x |
| Q9Y2W1 | THRAP3 | TR150_HUMAN | thyroid hormone receptor-associated protein 3 | 377 | EKIKEKGSFSDTGLG | x |
| Q9H0D6 | XRN2 | XRN2_HUMAN | 5′– 3′ exoribonuclease 2 | 678 | PEETRRNSLGGDVLF | x |
| P14625 | HSP90B1 | ENPL_HUMAN | endoplasmin (94 kDa glucose-regulated protein) (GRP-94) | 306 | AKEEKEESDDEAAVE | x |
| P48444 | ARCN1 | C0PD_HUMAN | coatomer subunit delta (delta-coat protein) | 437 | RHDSRRNTLEWCLPV | |
| Q5T5Y3 | CAMSAP1 | CAMP1_HUMAN | calmodulin-regulated spectrin-associated protein 1 | 629 | SIVSRRPSEGPQPLV | |
| 060716 | CTNND1 | CTND1_HUMAN | catenin delta-1 (cadherin-associated Src substrate) | 268 | PQVRVGGSSVDLHRF | |
| P12081 | HARS1 | HARS1_HUMAN | histidine-tRNA ligase, cytoplasmic | 27 | GLKQQKASAELIEEE | |
| P08670 | VIM | VIME_HUMAN | vimentin | 72 | SSAVRLRSSVPGVRL | |
| Q8WUI4 | HDAC7 | HDAC7_HUMAN | histone deacetylase 7 | 573 | CLRGRKASLEELQSV | |
| Q6P2E9 | EDC4 | EDC4_HUMAN | enhancer of mRNA-decapping protein 4 | 1389 | GKAARRLSLMLHGLV | |
| P53618 | C0PB1 | C0PB_HUMAN | coatomer subunit β (β-coat protein) | 933 | HIRIRAKSQGMALSL | |
| 095757 | HSPA4L | HS74L_HUMAN | heat shock 70 kDa protein 4L | 579 | LKKGKVKSIDLPIQS | |
| Q15149 | PLEC | PLEC_HUMAN | plectin | 2886 | PVRNRRLTVNEAVKE | |
| Q09666 | AHNAK | AHNK_HUMAN | neuroblast differentiation-associated protein AHNAK | 332 | PKAGLRVSAPEVSVG | |
| 000560 | SDCBP | SDCB1_HUMAN | syntenin-1 | 131 | KIGLRLKSIDNGIFV | |
| Q13501 | SQSTM1 | SQSTM_HUMAN | sequestosome-1 | 272 | RSRLTPVSPESSSTE | |
| Q15149 | PLEC | PLEC_HUMAN | plectin | 3785 | DYVRRRLTAEDLFEA | |
| P22626 | HNRNPA2B1 | R0A2_HUMAN | heterogeneous nuclear ribonucleoproteins A2/B1 | 225 | NFGPGPGSNFRGGSD | |
| P11586 | MTHFD1 | C1TC_HUMAN | C1-tetrahydrofolate synthase, cytoplasmic (C1-THF synthase) | 490 | VNGVRRFSDIQIRRL | |
| Q7Z406 | MYH14 | MYH14_HUMAN | myosin-14 (myosin heavy chain 14) | 105 | RMNPPKFSKAEDMAE | |
| 095613 | PCNT | PCNT_HUMAN | pericentrin | 1814 | ADQERRHSQALEALQ | |
| P35579 | MYH9 | MYH9_HUMAN | myosin-9 | 81 | KMNPPKFSKVEDMAE | |
| Q14980 | NUMA1 | NUMA1_HUMAN | nuclear mitotic apparatus protein 1 | 2047 | KQADRRQSMAFSILN | |
| P27816 | MAP-4 | MAP4_HUMAN | microtubule-associated protein 4 (MAP-4) | 636 | TGTGKKCSLPAEEDS | |
| P13861 | PRKAR2A | KAP2_HUMAN | cAMP-dependent protein kinase type II-α regulatory subunit | 58 | PAATPRQSLGHPPPE | |
| P98174 | FGD1 | FGD1_HUMAN | FYVE, RhoGEF, and PH domain-containing protein 1 | 135 | EGPQRLRSDPGPPTE | |
| P47897 | QARS1 | SYQ_HUMAN | glutamine-tRNA ligase | 70 | LRDTRRLSFLVSYIA | |
| Q8NDT2 | RBM15B | RB15B_HUMAN | putative RNA-binding protein 15B | 532 | ADLVRDRTPPHLLYS | |
| 095140 | MFN2 | MFN2_HUMAN | mitofusin-2 | 442 | AEEIRRLSVLVDDYQ | |
| 060832 | DKC1 | DKC1_HUMAN | H/ACA ribonucleoprotein complex subunit DKC1 | 21 | KKKKERKSLPEEDVA | |
| J-PKAca cells and FL-HCC | ||||||
|
| ||||||
| uniprot ID | gene name | entry name | protein name | site | sequence | directa |
| 043707 | ACTN4 | ACTN4_HUMAN | α-actinin-4 (nonmuscle α-actinin-4) | 423 | EKFRQKASIHEAWTD | xxx |
| 014579 | C0PE | C0PE_HUMAN | coatomer subunit epsilon | 99 | AHESRRDSIVAELDR | xx |
| P10809 | HSPD1 | CH60_HUMAN | 60 kDa heat shock protein, mitochondrial (Hsp60) | 488 | KNAGVEGSLIVEKIM | xx |
| Q14204 | DYNC1H1 | DYHC1_HUMAN | cytoplasmic dynein 1 heavy chain 1 | 1230 | DIMRRKDSAIQQQVA | xx |
| P07900 | HSP90AA1 | HS90A_HUMAN | heat shock protein HSP 90-α | 641 | LEINPDHSIIETLRQ | x |
| P21333 | FLN-A | FLNA_HUMAN | filamin-A (FLN-A) | 1084 | LQGGSAGSPARFTID | |
| Q16637 | SMN1 | SMN_HUMAN | survival motor neuron protein (Gemin-1) | 28 | FRRGTGQSDDSDIWD | |
| P61604 | HSPE1 | CH10_HUMAN | 10 kDa heat shock protein, mitochondrial (Hsp10) | 21 | DRVLVERSAAETVTK | |
| 060825 | PFKFB2 | F262_HUMAN | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2 | 466 | PVRMRRNSFTPLSSS | |
| Q12955 | ANK3 | ANK3_HUMAN | ankyrin-3 | 1459 | EKTDRRQSFASLALR | |
| P02545 | LMNA | LMNA_HUMAN | prelamin-A/C [cleaved into: lamin-A/C (70 kDa lamin)] | 392 | ERLRLSPSPTSQRSR | |
| Q9UI14 | RABAC1 | PRAF1_HUMAN | prenylated Rab acceptor protein 1 | 41 | WLERRRATIRPWSTF | |
| Q08211 | DHX9 | DHX9_HUMAN | ATP-dependent RNA helicase A | 1142 | IRQISRPSAAGINLM | |
| P83731 | RPL24 | RL24_HUMAN | 60S ribosomal protein L24 | 149 | IVKPVKVSAPRVGGK | |
| Q15126 | PMVK | PMVK_HUMAN | phosphomevalonate kinase (PMKase) | 113 | VSDTRRVSDIQWFRE | |
| J-PKAca cells and FL-HCC | ||||||
|
| ||||||
| uniprot ID | gene name | entry name | protein name | site | sequence | directa |
| Q9NZU5 | LMCD1 | LMCD1_HUMAN | LIM and cysteine-rich domains protein 1 | 16 | NPGVKKMSLGQLQSA | |
| Q8IVT5 | KSR1 | KSR1_HUMAN | kinase suppressor of Ras 1 | 888 | PKLNRRLSHPGHFWK | |
| 043707 | ACTN4 | ACTN4_HUMAN | α-actinin-4 (nonmuscle α-actinin-4) | 367 | LQTKLRLSNRPAFMP | |
| Q14789 | G0LGB1 | G0GB1_HUMAN | golgin subfamily B member 1 | 2489 | QLEERHLSIILEKDQ | |
| Q06210 | GFPT1 | GFPT1_HUMAN | glutamine-fructose-6-phosphate aminotransferase 1 | 205 | AVGTRRGSPLLIGVR | |
| 060488 | ACSL4 | ACSL4_HUMAN | long-chain-fatty-acid-CoA ligase 4 | 674 | IPIKVRLSPEPWTPE | |
| WT PKAca cells and FL-HCC | ||||||
|
| ||||||
| uniprot ID | gene name | entry name | protein name | site | sequence | directa |
| P11142 | HSPA8 | HSP7C_HUMAN | heat shock cognate 71 kDa protein | 329 | RDAKLDKSQIHDIVL | xx |
| P11142 | HSPA8 | HSP7C_HUMAN | heat shock cognate 71 kDa protein | 511 | TNDKGRLSKEDIERM | x |
| P78559 | MAP-1A | MAP1A_HUMAN | microtubule-associated protein 1A (MAP-1A) | 667 | EMEEVHPSDEEEEDA | |
| P17096 | HMGA1 | HMGA1_HUMAN | high mobility group protein HMG-I/HMG-Y | 102 | EEGISQESSEEEQ__ | |
| Q8NDT2 | RBM15B | RB15B_HUMAN | putative RNA-binding protein 15B | 609 | DRGRTTHSPYEERSR | |
| Q8WWI1 | LM0–7 | LM07_HUMAN | LIM domain only protein 7 (LMO-7) | 246 | RHHKREDSFESLDSL | |
| P27708 | CAD | PYR1_HUMAN | CAD protein (pyrimidine biosynthesis fusion complex) | 1406 | GAGGRRLSSFVTKGY | |
| Q16643 | DBN1 | DREB_HUMAN | drebrin | 142 | NGLARLSSPVLHRLR | |
| P49736 | MCM2 | MCM2_HUMAN | DNA replication licensing factor MCM2 | 139 | RRGLLYDSDEEDEER | |
| Q00610 | CLTC | CLH1_HUMAN | clathrin heavy chain 1 | 191 | YSVDRKVSQPIEGHA | |
| Q9NZB2 | FAM120A | F120A_HUMAN | constitutive coactivator of PPAR-γ-like protein 1 | 30 | LQKLARGSLVGGGRQ | |
| Q96S38 | RPS6KC1 | KS6C1_HUMAN | ribosomal protein S6 kinase delta-1 (S6K-delta-1) | 427 | LNRSPEESFDIKEVK | |
| Q9NNW5 | WDR6 | WDR6_HUMAN | WD repeat-containing protein 6 | 514 | VCGDRRGSVLLFPSR | |
| P02545 | LMNA | LMNA_HUMAN | prelamin-A/C [cleaved into: lamin-A/C (70 kDa lamin)] | 51 | VYIDRVRSLETENAG | |
| Q9UK76 | JPT1 | JUPI1_HUMAN | Jupiter microtubule-associated homologue 1 | 87 | SGLQRRNSSEASSGD | |
| Q8WX93 | PALLD | PALLD_HUMAN | palladin | 1121 | PRSRSRDSGDENEPI | |
| P46821 | MAP-1B | MAP1B_HUMAN | microtubule-associated protein 1B (MAP-1B) | 832 | AERSLMSSPEDLTKD | |
| Q5JRA6 | MIA3 | TG01_HUMAN | transport and Golgi organization protein 1 homologue (TANGO1) | 1539 | MALQKKLSQEEYERQ | |
| Q92905 | C0PS5 | CSN5_HUMAN | COP9 signalosome complex subunit 5 | 284 | EAQLGRGSFMLGLET | |
| Q02952 | AKAP12 | AKA12_HUMAN | A-kinase anchor protein 12 (AKAP12) | 627 | KKRVRRPSESDKEDE | |
| P21359 | NF-1 | NF1_HUMAN | neurofibromin (neurofibromatosis-related protein NF-1) | 2543 | KLLGTRKSFDHLISD | |
| Q9C0C9 | UBE20 | UBE20_HUMAN | (E3-independent) E2 ubiquitin-conjugating enzyme | 515 | SGTSRKKSIPLSIKN | |
| Q96S38 | RPS6KC1 | KS6C1_HUMAN | ribosomal protein S6 kinase delta-1 (S6K-delta-1) | 423 | ISKFLNRSPEESFDI | |
| Q6UX71 | PLXDC2 | PXDC2_HUMAN | plexin domain-containing protein 2 | 506 | AMKFRRGSGHPAYAE | |
| Q86UU1 | PHLDB1 | PHLB1_HUMAN | pleckstrin homology-like domain family B member 1 | 324 | GGHERPPSPGLRGLL | |
| 094806 | PRKD3 | KPCD3_HUMAN | serine/threonine-protein kinase D3 (protein kinase C nutype) | 731 | ARIIGEKSFRRSVVG | |
| A6NHR9 | SMCHD1 | SMHD1_HUMAN | structural maintenance of chromosomes flexible hinge domain-containing protein 1 | 1697 | ALLKRKLSEQEELKK | |
| Q15084 | PDIA6 | PDIA6_HUMAN | protein disulfide-isomerase A6 | 428 | VEDDIDLSDVELDDL | |
a
Number of direct phosphorylation observations at the protein or peptide level (see Supporting Table S1).