Table 5.
Classification of the proteins that were found to be differentially abundant (left) or differentially phosphorylated (right) for patient populations with >0.01% clonogenic cells. The proteins with higher abundance are associated with transcription and lipid/ion transport. The differentially phosphorylated proteins, on the other hand, are mainly linked with protein biosynthesis and the cytoskeleton. For details on the proteins, see Supplementary Tables S12 and S13.
| Biological Process | Proteomic Analysis | Phosphoproteomic Analysis | ||
|---|---|---|---|---|
| Increased ≥200 Colonies | Decreased ≥200 Colonies | Increased ≥200 Colonies | Decreased ≥200 Colonies | |
| mRNA splicing | RBMXL1; TXNL4A; ZNF830 | PCBP1 2 | PAPOLA; PRPF31; PRPF40A | |
| Transcription | MED1; POLR3C; ZNF830 | SMG1 2 | DOT1L 2; TCEAL3; ZNF521 2 | CBFB 2; ISL2; LEO1 2; MYSM1 |
| Transcription repressor | SPEN; ZNF521 2 | AEBP2 2; GATAD2B | ||
| Translation | ABCF1; EIF2B2; FARSB; MRPL3 | DNAJC2; EIF5B | ||
| Kinase | CAMK2D; DGKZ; SMG1 2 | NEK1; PRKD2 | ||
| Chaperone | DNAJC2; DNAJC5 | |||
| Metabolism | CPD 1; HEXB; MPDU1 | USP4 | CAST 2; CPD 1; DOT1L 2 | CTPS1; MYO9B; PPP6R3; RASGRP2 |
| Transporter, ion channel | CLIC4; CPD 1; CRIP1; RALGAPA2 | ABCF1; CLCN3; RBP4 | CPD | ATP13A1; OSBP; SCAP |
| Signaling | RALGAPA2; VIM 1,2 | CAP1; MRC2 | VIM 1,2; ZFYVE26 | LAT 2; LSP12; mTOR 2; RNF31; TMPO |
| Cytoskeleton | VIM 1,2 | AAMP; CAP1; MYOF | SP100; VIM 1,2; ZFYVE26 | DBNL; MYO9B; SH3BP1; TMPO |
| Apoptosis | MED1; RMDN3; TMEM173 | GRAMD4; MAP1S 2 | ||
| Cell cycle/mitosis | KIF4A | NEK1 | ||
| Proliferation regulation | FAM53C; SCRIB | |||
| Others | C19orf19/TRIR; MOB4 | BOD1L1; CAD; IRF2BP2; TTC7A | ||
| Unknown | GPALPP1 | MAP7D1 1 | MAP7D1 1; TOR4A | |
1 These proteins are found in both proteomic and phosphoproteomic analysis. 2 These proteins have been studied in AML.