Relative proteomic analysis of the effects of atRA on protein expression in HepG2 cells
The changes were quantified via spectral counting. Significant differences are underlined. Only proteins for which the same peptide was consistently detected in all replicate control and treated samples are shown.
| UniProt ID | RA/Con | P value | Protein Name | Gene Name | |
|---|---|---|---|---|---|
| Transcription | Q92804 | 1.00 | 1.00 | TATA-binding protein-associated factor 2N | TAF15 |
| P12004 | 0.93 | 0.23 | Proliferating cell nuclear antigen | PCNA | |
| P20290 | 1.21 | 0.02 | Transcription factor BTF3 | BTF3 | |
| Q13185 | 0.88 | 0.02 | Chromobox protein homolog 3 | CBX3 | |
| Q08211 | 1.51 | 0.04 | ATP-dependent RNA helicase A | DHX9 | |
| RNA Processing | O43776 | 1.15 | 0.33 | Asparagine–tRNA ligase, cytoplasmic | NARS |
| Q99714 | 0.63 | 0.15 | 3-hydroxyacyl-CoA dehydrogenase type-2 | HSD17B10 | |
| O75643 | 1.70 | 0.004 | U5 small nuclear ribonucleoprotein 200 kDa helicase | SNRNP200 | |
| P31942 | 1.91 | 0.008 | Heterogeneous nuclear ribonucleoprotein H3 | HNRNPH3 | |
| Q1KMD3 | 1.36 | 0.01 | Heterogeneous nuclear ribonucleoprotein U-like protein 2 | HNRNPUL2 | |
| P55795 | 0.70 | 0.01 | Heterogeneous nuclear ribonucleoprotein H2 | HNRNPH2 | |
| P23246 | 1.20 | 0.03 | Splicing factor, proline- and glutamine-rich | SFPQ | |
| Q16630 | 1.30 | 0.03 | Cleavage and polyadenylation specificity factor subunit 6 | CPSF6 | |
| P49588 | 1.32 | 0.03 | Alanine-tRNA ligase, cytoplasmic | AARS | |
| Q15637 | 1.40 | 0.04 | Splicing factor 1 | SF1 | |
| Translation | P46779 | 0.52 | 0.01 | 60S ribosomal protein L28 | RPL28 |
| P56537 | 0.96 | 0.77 | Eukaryotic translation initiation factor 6 | EIF6 | |
| P62241 | 0.80 | 0.02 | 40S ribosomal protein S8 | RPS8 | |
| Q9NR30 | 1.32 | 0.01 | Nucleolar RNA helicase 2 | DDX21 | |
| P24534 | 1.28 | 0.02 | Elongation factor 1-beta | EEF1B2 | |
| P26373 | 0.73 | 0.03 | 60S ribosomal protein L13 | RPL13 | |
| Protein integrity | P61604 | 0.78 | 0.27 | 10 kDa heat shock protein, mitochondrial | HSPE1 |
| Q9Y3C6 | 0.95 | 0.42 | Peptidyl-prolyl cis-trans isomerase-like 1 | PPIL1 | |
| P13667 | 1.18 | 0.02 | Protein disulfide-isomerase A4 | PDIA4 | |
| P27797 | 1.24 | 0.03 | Calreticulin | CALR | |
| P08107 | 2.70 | 0.03 | Heat shock 70 kDa protein 1A/1B | HSPA1A | |
| Q9Y4L1 | 1.50 | 0.03 | Hypoxia upregulated protein 1 | HYOU1 | |
| P11021 | 0.93 | 0.04 | 78 kDa glucose-regulated protein | HSPA5 | |
| P08238 | 1.13 | 0.04 | Heat shock protein HSP 90-beta | HSP90AB1 | |
| Protease activity | P49720 | 0.90 | 0.69 | Proteasome subunit beta type-3 | PSMB3 |
| Q99436 | 0.75 | 0.29 | Proteasome subunit beta type-7 | PSMB7 | |
| P35998 | 1.20 | 0.02 | 26S protease regulatory subunit 7 | PSMC2 | |
| P55036 | 1.21 | 0.04 | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4 | |
| Cellular trafficking | Q9Y678 | 0.85 | 0.11 | Coatomer subunit gamma-1 | COPG1 |
| Q8TEX9 | 1.28 | 0.03 | Importin-4 | IPO4 | |
| Q14974 | 1.15 | 0.004 | Importin subunit beta-1 | KPNB1 | |
| P51149 | 1.37 | 0.03 | Ras-related protein Rab-7a | RAB7A | |
| O00151 | 1.30 | 0.04 | PDZ and LIM domain protein 1 | PDLIM1 | |
| Metabolism | P23526 | 1.05 | 0.59 | Adenosylhomocysteinase | AHCY |
| O60701 | 0.93 | 0.16 | UDP-glucose 6-dehydrogenase | UGDH | |
| P51659 | 1.30 | 0.49 | Peroxisomal multifunctional enzyme type 2 | HSD17B4 | |
| P40925 | 1.01 | 0.72 | Malate dehydrogenase, cytoplasmic | MDH1 | |
| Q15181 | 1.22 | 0.26 | Inorganic pyrophosphatase | PPA1 | |
| Q9NR45 | 0.98 | 0.89 | Sialic acid synthase | NANS | |
| O43175 | 1.03 | 0.53 | D-3-phosphoglycerate dehydrogenase | PHGDH | |
| Q8NF37 | 1.00 | 1.00 | Lysophosphatidylcholine acyltransferase 1 | LPCAT1 | |
| P54819 | 1.03 | 0.64 | Adenylate kinase 2, mitochondrial | AK2 | |
| Q06830 | 1.02 | 0.685 | Peroxiredoxin-1 | PRDX1 | |
| P14324 | 1.52 | 0.01 | Farnesyl pyrophosphate synthase | FDPS | |
| Q99541 | 2.57 | 0.001 | Perilipin-1 | PLIN2 | |
| P49327 | 1.27 | 0.002 | Fatty acid synthase | FASN | |
| P06737 | 2.46 | 0.00 | Glycogen Phosphorylase, liver form | PYGL | |
| Q13011 | 1.27 | 0.006 | Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial | ECH1 | |
| Q95573 | 1.56 | 0.01 | Long-chain-fatty-acid-CoA ligase 3 | ACSL3 | |
| P17174 | 2.11 | 0.01 | Aspartate aminotransferase, cytoplasmic | GOT1 | |
| P49419 | 1.74 | 0.01 | Alpha-aminoadipic semialdehyde dehydrogenase | ALDH7A1 | |
| Q86SX6 | 2.26 | 0.01 | Glutaredoexin-related protein 5, mitochondrial | GLRX5 | |
| P12268 | 1.50 | 0.01 | Inosine-5′-monophosphate dehydrogenase 2 | IMPDH2 | |
| Q53HR2 | 1.68 | 0.01 | Acyl-Coenzyme A dehydrogenase | ACAD | |
| P25705 | 1.56 | 0.02 | ATP synthase subunit alpha, mitochondrial | ATP5A1 | |
| Q8NBX0 | 1.35 | 0.02 | Saccharopine dehydrogenase-like oxidoreductase | SCCPDH | |
| O60448 | 1.38 | 0.02 | Long-chain-fatty-acid-CoA ligase 4 | ACSL4 | |
| P05091 | 1.24 | 0.03 | Aldehyde dehydrogenase, mitochondrial | ALDH2 | |
| P48735 | 1.67 | 0.03 | Isocitrate dehydrogenase [NADP], mitochondrial | IDH2 | |
| P51648 | 1.88 | 0.03 | Fatty aldehyde dehydrogenase | ALDH3A2 | |
| P52209 | 1.44 | 0.03 | 6-phosphogluconate dehydrogenase, decarboxylating | PGD | |
| P00387 | 1.29 | 0.03 | NADH-cytochrome b5 reductase 3 | CYB5R3 | |
| P12277 | 1.38 | 0.04 | Creatine kinase B- type | CKB | |
| P80404 | 2.00 | 0.04 | 4-aminobutyrate aminotransferase, mitochondrial | ABAT | |
| P78417 | 1.34 | 0.04 | Glutathione S-transferase omega-1 | GSTO1 | |
| P50897 | 1.62 | 0.04 | Palmitoyl-protein thioesterase 1 | PPT1 | |
| P11586 | 1.28 | 0.04 | C-1-tetrahydrofolate synthase, cytoplasmic | MTHFD1 | |
| Cell cycle regulation | P42166 | 0.85 | 0.67 | Thymopoietin isoform alpha | TMPO |
| P33991 | 1.45 | 0.13 | DNA replication licensing factor MCM4 | MCM4 | |
| P33993 | 0.94 | 0.67 | DNA replication licensing factor MCM7 | MCM7 | |
| P49736 | 1.47 | 0.004 | DNA replication licensing factor MCM2 | MCM2 | |
| P62826 | 1.14 | 0.04 | GTP-binding nuclear protein Ran | RAN | |
| P18754 | 1.35 | 0.01 | Regulator of chromosome condensation | RCC1 | |
| Cell survival | O75874 | 1.20 | 0.08 | Isocitrate dehydrogenase [NADP] cytoplasmic | IDH1 |
| P38646 | 1.21 | 0.04 | Stress-70 protein, mitochondrial | HSPA9 | |
| Q13442 | 1.78 | 0.01 | 28 kDa heat- and acid-stable phosphoprotein | PDAP1 | |
| Apoptosis | P10599 | 1.00 | 1.00 | Thioredoxin | TXN |
| P21796 | 1.28 | 0.01 | Voltage-dependent anion-selective channel protein 1 | VDAC1 | |
| P09382 | 0.95 | 0.64 | Galectin-1 | LGALS1 | |
| Q9Y265 | 1.00 | 1.00 | RuvB-like 1 | RUVBL1 | |
| Structural integrity | P15924 | 0.93 | 0.28 | Desmoplakin | DSP |
| Q09666 | 1.64 | 0.19 | Neuroblast differentiation-associated protein AHNAK | AHNAK | |
| Q15149 | 0.85 | 0.32 | Plectin | PLEC | |
| Q01082 | 1.02 | 0.89 | Spectrin beta chain | SPTBN1 | |
| P63313 | 0.72 | 0.10 | Thymosin beta-10 | TMSB10 | |
| Q9Y2B0 | 1.09 | 0.39 | Protein canopy homolog 2 | CNPY2 | |
| P35579 | 2.61 | 0.02 | Myosin-9 | MYH9 | |
| P67936 | 2.58 | 0.01 | Tropomyosin alpha-4 chain | TPM4 | |
| Misc. | P08758 | 1.12 | 0.31 | Annexin A5 | ANXA5 |
| Q13283 | 1.19 | 0.41 | Ras GTPase-activating protein-binding protein 1 | G3BP1 | |
| Q96CN7 | 0.72 | 0.23 | Isochorismatase domain-containing protein 1 | ISOC1 | |
| Q9H3K6 | 1.38 | 0.30 | BolA-like protein 2 | BOLA2 |
ACAD, fatty acyl CoA dehydrogenase; ATP5A1, ATP synthase subunit α.