TABLE 1.
Biotin concentrations in culture media affect the abundance of protein clusters in HepG2 cells
| Treatment (biotin in culture medium)1 |
|||
|---|---|---|---|
| Protein cluster2 | Confidence level3 | Deficient | Pharmacological |
| Protein abundance (compared with physiological controls)1 | |||
| Cell signaling | |||
| GRB2 | 10 | Increase | |
| Sam68 | 10 | Increase | |
| AF6 | 10 | Decrease | |
| Annexin II | 10 | Decrease | |
| A-RAF | 9 | Increase | |
| TNIK | 9 | Decrease | |
| CDC42GAP | 8 | Decrease | Decrease4 |
| PSD-95 | 8 | Decrease | |
| Tpl-2 | 8 | Decrease | Decrease4 |
| GAP1m | 8 | Decrease | |
| IRS-1 | 7 | Decrease | |
| c-Cbl | 7 | Increase | |
| Nucleus and nuclear transport | |||
| Ku70 | 9 | Decrease | |
| Smad4/DPC4 | 8 | Decrease | |
| ICBP90 | 7 | Decrease | |
| No55 | 7 | Increase | |
| RanBP3 | 7 | Decrease | |
| Stat2 | 7 | Increase | |
| hSlu7 | 7 | Decrease | |
| FIP-2 | 7 | Decrease | |
| CTCF | 7 | Increase | |
| TIP49b | 7 | Decrease | |
| Cytoskeleton | |||
| E-Cadherin | 9 | Decrease | |
| EBP50 | 9 | Decrease | |
| Gelsolin | 8 | Increase | |
| EB1 | 7 | Increase | |
| CLP-36 | 7 | Decrease | |
| L-caldesmon | 7 | Decrease | |
| Neuroscience | |||
| Amphiphysin | 8 | Decrease | Decrease4 |
| Nogo A | 8 | Decrease | Decrease4 |
| b1-Calcium channel | 8 | Decrease | Decrease4 |
| Nurr | 7 | Decrease | |
| Syntaxin 4 | 7 | Increase | |
| PCMT-I/II | 7 | Increase | |
| Cell biology | |||
| mEPHX | 10 | Decrease | |
| ATP synthase b | 9 | Decrease | |
| GGA2 | 9 | Decrease | |
| Bpntase | 7 | Decrease | |
| LR11/SorLA | 9 | Increase | |
| Others | |||
| E-Cadherin | 9 | Decrease | |
| eIF-4F | 7 | Increase | |
| LRP | 7 | Increase | |
| FKBP65 | 7 | Decrease | |
| CDC27 | 7 | Increase | |
1
HepG2 cells were cultured in media containing 0.025 nmol/L biotin (“deficient”), 0.25 nmol/L biotin (“physiological” = control), and 10 nmol/L biotin (“pharmacological”) for 10 d.
2
SwissProt IDs of proteins are provided in the Appendix.
3
The “Confidence level” is a measure for data quality on a scale from 1 to 10 (10 being the highest; see Materials and Methods for Details).
4
The abundance of this protein decreased in response to both deficient and pharmacological concentrations of biotin compared with physiological controls.