Table 1. Proteins Associated with DNA Replication that Respond Strongly to CDC7 Knockdowna.
| Consensus | DNA Replication Network | Cytoplasm | Nucleus | Total lysate | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene Name | Unique Peptides | Gene Mania | String | Reactome | SILAC Ratio | SigB | Ratio Count | SILAC Ratio | SigB | Ratio Count | SILAC Ratio | SigB | Ratio Count |
|
Strict proteins found by programmatic network analysis
| |||||||||||||
| CDK1 (CDC2) | 11 | • | • | • | 0.39 | 5.19E-11 | 33 | 0.40 | 6.66E-04 | 22 | ND | ND | ND |
| CDKN1A | 4 | • | • | • | 3.47 | 1.16E-06 | 18 | 1.16 | 3.91E-01 | 16 | ND | ND | ND |
| DUT | 8 | • | • | • | 0.34 | 1.66E-05 | 44 | 0.28 | 5.16E-06 | 16 | NaN | NaN | 2 |
| FEN1 | 7 | • | • | • | 0.92 | 7.18E-01 | 12 | 0.43 | 1.62E-03 | 17 | 0.43 | 2.83E-03 | 3 |
| HAT1 | 9 | • | 1.21 | 4.51E-01 | 13 | 0.34 | 7.88E-06 | 12 | ND | ND | ND | ||
| KPNA2 | 13 | • | • | 0.37 | 1.36E-06 | 40 | 0.36 | 1.04E-04 | 28 | 0.38 | 4.95E-04 | 13 | |
| MAD2L1 | 6 | • | • | • | 0.38 | 7.87E-06 | 11 | 0.52 | 3.87E-02 | 10 | ND | ND | ND |
| MCM2 | 21 | • | • | • | 1.78 | 2.75E-02 | 11 | 0.36 | 8.09E-07 | 45 | NaN | NaN | 2 |
| MCM3 | 24 | • | • | • | 0.47 | 5.12E-04 | 4 | 0.39 | 4.22E-04 | 46 | ND | ND | ND |
| MCM4 | 19 | • | • | • | 0.74 | 1.43E-01 | 3 | 0.42 | 1.26E-03 | 33 | ND | ND | ND |
| MCM5 | 15 | • | • | • | 0.98 | 9.14E-01 | 7 | 0.39 | 3.84E-04 | 21 | ND | ND | ND |
| MCM6 | 24 | • | • | • | 0.53 | 3.13E-03 | 6 | 0.35 | 8.85E-05 | 39 | ND | ND | ND |
| MCM7 | 21 | • | • | • | 0.60 | 4.05E-02 | 7 | 0.35 | 5.93E-05 | 37 | 0.26 | 1.89E-06 | 3 |
| NASP | 16 | • | • | 0.67 | 5.99E-02 | 28 | 0.30 | 4.60E-06 | 27 | 0.51 | 1.64E-02 | 5 | |
| PCNA | 12 | • | • | • | 0.93 | 7.42E-01 | 60 | 0.37 | 1.77E-06 | 49 | 0.49 | 2.37E-04 | 40 |
| PSME3 | 9 | • | • | • | 2.35 | 1.10E-04 | 29 | 0.61 | 8.03E-02 | 45 | 0.92 | 7.94E-01 | 17 |
| RBM14 | 13 | • | • | ND | ND | ND | 0.65 | 1.28E-01 | 31 | 0.30 | 1.88E-05 | 8 | |
| RRM1 | 17 | • | • | • | 0.52 | 1.46E-03 | 29 | 0.45 | 4.12E-03 | 5 | 0.59 | 5.16E-02 | 5 |
| RRM2 | 6 | • | • | • | 0.25 | 5.39E-08 | 19 | ND | ND | ND | ND | ND | ND |
| SET | 6 | • | • | 3.14 | 1.08E-10 | 41 | 0.60 | 1.99E-02 | 43 | 0.97 | 8.67E-01 | 39 | |
| STMN1 | 8 | • | • | 0.52 | 4.84E-06 | 70 | 0.41 | 8.59E-04 | 34 | 0.68 | 7.22E-02 | 31 | |
| TK1 | 8 | • | • | • | 0.27 | 2.79E-07 | 15 | NaN | NaN | 2 | ND | ND | ND |
| TYMS | 9 | • | • | • | 0.31 | 4.38E-06 | 23 | 0.27 | 1.78E-05 | 3 | ND | ND | ND |
| YWHAZ | 13 | • | 0.61 | 8.66E-04 | 178 | 0.56 | 7.96E-03 | 95 | 0.90 | 8.02E-01 | 131 | ||
|
| |||||||||||||
|
Strict proteins based on literature evidence
| |||||||||||||
| KPNB1 | 32 | 0.59 | 3.04E-04 | 153 | 0.65 | 6.06E-02 | 119 | 0.84 | 5.37E-01 | 90 | |||
| PC4 (SUB1) | 6 | 0.46 | 1.72E-04 | 32 | 1.53 | 7.94E-03 | 35 | 1.16 | 4.78E-01 | 22 | |||
| XRCC5 | 31 | 2.28 | 2.80E-06 | 53 | 0.68 | 9.62E-02 | 108 | 0.89 | 6.85E-01 | 37 | |||
| XRCC6 | 29 | 2.43 | 4.78E-07 | 72 | 0.66 | 6.32E-02 | 133 | 0.85 | 5.68E-01 | 83 | |||
|
| |||||||||||||
|
Additional proteins under “relaxed” selection criteria
| |||||||||||||
| CDK2 | 7 | • | • | 0.61 | 4.93E-02 | 15 | 0.44 | 4.07E-03 | 11 | ND | ND | ND | |
| CDK4 | 7 | • | • | 1.67 | 4.99E-02 | 9 | ND | ND | ND | 2.14 | 1.73E-02 | 5 | |
| CDK6 | 6 | • | • | 0.43 | 2.02E-03 | 6 | NaN | NaN | 2 | ND | ND | ND | |
| CDKN2A | 3 | • | • | 1.32 | 4.49E-01 | 5 | ND | ND | ND | 6.23 | 2.81E-09 | 6 | |
| DHFR | 3 | • | • | • | 0.31 | 2.79E-05 | 10 | NaN | NaN | 2 | ND | ND | ND |
| DTYMK | 15 | • | 0.64 | 3.62E-02 | 40 | 0.60 | 7.71E-02 | 16 | 0.68 | 1.81E-01 | 18 | ||
| H2AFV,H2AFZ | 2 | • | 0.65 | 8.73E-02 | 10 | 0.81 | 4.28E-01 | 67 | 0.59 | 5.86E-02 | 18 | ||
| MSH2 | 7 | • | ND | ND | ND | 0.65 | 1.50E-01 | 12 | ND | ND | ND | ||
| MSH6 | 9 | • | ND | ND | ND | 0.57 | 2.98E-02 | 10 | ND | ND | ND | ||
| NCAPD2 | 9 | • | 0.56 | 5.86E-03 | 9 | ND | ND | ND | ND | ND | ND | ||
| NCAPG | 10 | • | 0.53 | 2.46E-03 | 12 | 0.65 | 1.74E-01 | 3 | ND | ND | ND | ||
| NES | 1 | • | ND | ND | ND | 1.01 | 7.38E-01 | 7 | 0.57 | 2.62E-02 | 14 | ||
| PBK | 6 | • | 0.35 | 9.58E-07 | 7 | NaN | NaN | 1 | ND | ND | ND | ||
| PDS5A | 10 | • | ND | ND | ND | 0.63 | 9.74E-02 | 15 | ND | ND | ND | ||
| RANGAP1 | 24 | • | 0.94 | 7.87E-01 | 47 | 0.79 | 3.51E-01 | 52 | 0.60 | 1.45E-02 | 74 | ||
| RECQL | 20 | • | 1.85 | 1.02E-02 | 7 | 0.87 | 6.81E-01 | 55 | ND | ND | ND | ||
| SMC2 | 19 | • | • | 0.58 | 2.97E-02 | 17 | 0.43 | 4.70E-04 | 11 | ND | ND | ND | |
| T0P2A | 11 | • | • | ND | ND | ND | 0.34 | 5.42E-05 | 14 | ND | ND | ND | |
|
| |||||||||||||
|
Protein complexes
| |||||||||||||
| RFC1 | 2 | • | • | ND | ND | ND | 0.56 | 6.43E-02 | 4 | ND | ND | ND | |
| RFC2 | 8 | • | • | 0.96 | 7.61E-01 | 8 | 0.62 | 7.40E-02 | 14 | ND | ND | ND | |
| RFC3 | 7 | • | • | • | ND | ND | ND | 0.55 | 2.06E-02 | 13 | ND | ND | ND |
| RFC4 | 10 | • | • | • | NaN | NaN | 2 | 0.61 | 6.06E-02 | 18 | NaN | NaN | 0 |
| RFC5 | 12 | • | • | NaN | NaN | 2 | 0.59 | 6.03E-02 | 25 | ND | ND | ND | |
|
| |||||||||||||
| RPA1 | 11 | • | • | 0.82 | 3.17E-01 | 8 | 0.62 | 1.36E-01 | 5 | ND | ND | ND | |
| RPA2 | 6 | • | • | 0.78 | 2.26E-01 | 7 | 0.66 | 1.63E-01 | 7 | ND | ND | ND | |
| RPA3 | 4 | • | • | • | 0.81 | 3.91E-01 | 9 | 0.55 | 6.02E-02 | 6 | ND | ND | ND |
a
Details of protein names, sequences, etc. are given in Supplementary Table 4, Supporting Information. Shading indicates the criterion used to include the protein (see Material and Methods): (blue) St, (green) Sn and/or Sc, (red) log2(Sn/Sc), (orange) relaxed (see text). ND denotes proteins not detected. NaN denotes proteins not quantified.