Table 2. List of quantified proteins involved in the phagosome and antigen presentation pathways.
The values are Log2-transformed abundance ratios between sample pairs. Abundance ratios in bold are statistically significant (see Methods).
| In Mφs | In DCs | In Mφs vs in DCs | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene symbol |
Protein description |
Phagosome pathway components |
Spectral counts | Peptide counts | ΦMφ,KO/ΦMφ,H37Rv | ΦMφ,KO/ΦMφ,BCG | ΦMφ,H37Rv/ΦMP,BCG | ΦDC,KO/ΦDC,H37Rv | ΦDC,KO/ΦDC,BCG | ΦDC,H37Rv/ΦDC,BCG | ΦMφ,KO/ΦDC,KO | ΦMφ,H37Rv/ΦDC,H37Rv | ΦMφ,BCG/ΦDC,BCG | WCMφ/ WCDC |
| Actg1 | actin, gamma, cytoplasmic 1 | F-actin | 7136 | 26 | −0.6 | 0.1 | 0.7 | −0.4 | 0.0 | 0.4 | −0.3 | −0.1 | −0.4 | 0.4 |
| Atp6v0c | ATPase, H+ transporting, lysosomal V0 subunit C | vATPase | 10 | 1 | 12 | 0.8 | −11 | −0.7 | −7.9 | −7.1 | 13 | 1.0 | 4.6 | 11.0 |
| Atp6v1a | ATPase, H+ transporting, lysosomal V1 subunit A | 32 | 6 | −1.3 | 0.8 | 2.1 | −2.9 | −1.7 | 1.1 | 1.0 | −0.5 | −1.6 | 0.7 | |
| Atp6v1b2 | ATPase, H+ transporting, lysosomal V1 subunit B2 | 12 | 5 | 1.4 | 0.6 | −0.8 | 3.6 | 0.5 | −3.2 | 0.4 | 2.7 | 0.3 | 1.4 | |
| Atp6v1e1 | ATPase, H+ transporting, lysosomal V1 subunit E1 | 57 | 7 | 1.7 | −0.2 | −1.9 | −3.5 | 1.2 | 4.7 | 3.1 | −2.0 | 4.5 | −2.1 | |
| Atp6v1f | ATPase, H+ transporting, lysosomal V1 subunit F | 1 | 1 | −8.2 | −7.0 | 1.2 | 1.0 | 1.3 | 0.2 | −7.3 | 1.9 | 0.9 | −8.7 | |
| Calr | calreticulin | CALR | 477 | 14 | −1.2 | −0.6 | 0.6 | 0.8 | −1.0 | −1.7 | 0.1 | 2.1 | −0.3 | −1.7 |
| Cd14 | CD14 antigen | Toll-like receptor | 25 | 4 | −1.4 | 2.3 | 3.7 | 0.0 | −0.2 | −0.2 | 1.0 | 2.4 | −1.5 | 3.7 |
| Coro1a | coronin, actin binding protein 1A | coronin | 44 | 2 | −2.0 | −7.4 | −5.4 | −0.3 | −2.7 | −2.4 | −11 | −9.7 | −6.7 | −4.9 |
| Ctss | cathepsin S | cathepsin | 28 | 2 | 3.7 | 0.0 | −3.7 | 1.4 | 2.9 | 1.4 | 2.2 | −0.1 | 5.1 | −0.6 |
| Dync1h1 | Dynein cytoplasmic 1 heavy chain 1 | Dynein | 204 | 29 | −0.2 | 0.1 | 0.3 | −1.0 | −0.2 | 0.9 | 0.0 | −0.8 | −0.2 | −0.2 |
| Dync1i2 | Dynein cytoplasmic 1 intermediate chain 2 | 2 | 1 | −2.0 | −0.4 | 1.6 | −3.1 | −1.9 | 1.1 | −0.3 | −1.3 | −1.8 | −5.3 | |
| H2-Ab1 | histocompatibility 2, class II antigen A, beta 1 | MHCII | 17 | 2 | 12 | −1.8 | −14 | 9.6 | 8.4 | −1.2 | 3.3 | 1.0 | 14 | 0.0 |
| H2-Eb1 | histocompatibility 2, class II antigen E beta | 7 | 1 | 11 | 0.2 | −11 | −10 | −1.9 | 8.3 | 13 | −8.5 | 11 | −0.3 | |
| H2K1 | histocompatibility 2, K1, K region | MHCI | 9 | 5 | −3.5 | −3.3 | 0.1 | −2.2 | −3.3 | −1.1 | −2.0 | −0.8 | −2.0 | −1.1 |
| H2-Q1 | histocompatibility 2, Q region locus 1 | 19 | 2 | 2.3 | 1.3 | −1.0 | 6.2 | 12 | 5.9 | 0.3 | 4.2 | 11 | 0.2 | |
| H2-T10 | histocompatibility 2, T region locus 10 | 2 | 2 | −1.8 | −0.2 | 1.6 | −0.4 | −0.4 | 0.0 | −0.1 | 1.4 | −0.3 | 3.9 | |
| Itgb1 | integrin beta 1 (fibronectin receptor beta) | integrin | 3 | 3 | −3.0 | −0.6 | 2.4 | −3.4 | −4.5 | −1.1 | 1.0 | 0.6 | −2.9 | 1.8 |
| Itgam | integrin alpha M | Complement | 64 | 8 | 1.1 | 0.2 | −0.9 | −0.5 | 1.3 | 1.8 | 0.4 | −1.2 | 1.5 | 2.0 |
| Itgb2 | integrin beta 2 | receptors | 81 | 5 | 1.5 | 0.6 | −0.9 | 6.0 | 2.3 | −3.7 | −0.3 | 4.2 | 1.5 | −1.1 |
| Lamp2 | lysosomal-associated membrane protein 2 | LAMP | 49 | 6 | 1.9 | −0.4 | −2.3 | 1.9 | 1.7 | −0.2 | 1.0 | 1.0 | 3.1 | 1.4 |
| M6pr | mannose-6-phosphate receptor, cation dependent | M6PR | 20 | 2 | 13 | 5.0 | −7.5 | −0.7 | −1.9 | −1.2 | 14 | 1.0 | 7.3 | 6.5 |
| Msr1 | macrophage scavenger receptor 1 | Scavenger receptors | 2 | 1 | 3.3 | 8.8 | 5.6 | −0.7 | −1.9 | −1.2 | 8.9 | 4.9 | −1.8 | 0.2 |
| Ncstn | Nicastrin | gamma-secretase | 4 | 1 | 3.1 | 5.0 | 1.9 | −2.8 | 0.1 | 2.9 | 5.4 | −0.5 | 0.5 | 4.8 |
| Rab5c | RAB5C, member RAS oncogene family | Rab5 | 33 | 3 | 0.6 | 0.0 | −0.5 | 2.2 | 3.0 | 0.8 | −1.8 | −0.1 | 1.2 | −1.7 |
| Rab7 | RAB7, member RAS oncogene family | Rab7 | 121 | 5 | 0.5 | 0.0 | −0.5 | 0.4 | −0.1 | −0.5 | 1.0 | 0.9 | 0.9 | 1.3 |
| Ncf1 | neutrophil cytosolic factor 1 | NADPH oxidase | 9 | 2 | 0.0 | −0.9 | −1.0 | 2.6 | 3.4 | 0.9 | −1.7 | 0.8 | 2.6 | 3.1 |
| Rac1 | RAS-related C3 botulinum substrate 1 | 76 | 6 | −0.7 | 0.0 | 0.7 | 5.4 | 4.3 | −1.2 | −2.4 | 3.8 | 1.9 | 1.3 | |
| Sec22b | SEC22 vesicle trafficking protein homolog B (S. cerevisiae) | Sec22 | 25 | 3 | 5.1 | 0.1 | −5.0 | 1.6 | 2.8 | 1.3 | 1.8 | −1.7 | 4.5 | 3.0 |
| Tap1 | transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) | TAP | 4 | 1 | 1.6 | 1.6 | 0.0 | −2.4 | −0.4 | 2.0 | 4.5 | 0.5 | 2.5 | 2.0 |
| Tap2 | transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) | 7 | 3 | −1.1 | 1.0 | 2.1 | 0.9 | −1.3 | −2.2 | 3.1 | 5.1 | 0.8 | 3.8 | |
| Tfrc | transferrin receptor | TfR | 6 | 1 | −1.5 | 1.9 | 3.4 | −2.4 | 8.1 | 11 | −0.3 | −1.2 | 5.9 | −7.7 |
| Tuba1a | tubulin, alpha 1A | TUBA | 10 | 2 | 0.3 | 3.1 | 2.7 | −2.7 | 1.6 | 4.4 | 5.4 | 2.3 | 3.9 | 1.7 |
| Tuba1b | tubulin, alpha 1B | 560 | 12 | −0.4 | −0.4 | −0.1 | −0.2 | 0.2 | 0.4 | 0.0 | 0.2 | 0.6 | 0.4 | |
| Tubb1 | tubulin, beta 1 | TUBB | 1 | 1 | −11 | −0.4 | 11 | 5.6 | −4.3 | −9.9 | −6.6 | 10 | −11 | −4.0 |
| Tubb2a | tubulin, beta 2A | 4 | 2 | −2.7 | −0.2 | 2.5 | −4.9 | −1.3 | 3.6 | 2.7 | 0.5 | 1.5 | −0.8 | |
| Tubb2c | tubulin, beta 2C | 13 | 4 | −6.0 | 1.0 | 7.0 | 4.7 | 7.1 | 2.4 | −3.1 | 7.5 | 3.0 | −2.0 | |
| Tubb3 | tubulin, beta 3 | 6 | 3 | −7.7 | −5.0 | 2.7 | −1.3 | 7.6 | 8.9 | −2.8 | 3.6 | 9.8 | −1.6 | |
| Tubb4 | tubulin, beta 4 | 91 | 5 | 0.3 | −1.2 | −1.5 | 1.3 | 4.6 | 3.3 | 1.0 | 2.0 | 6.8 | 2.0 | |
| Tubb5 | tubulin, beta 5 | 696 | 20 | −1.0 | −0.5 | 0.5 | −1.3 | 1.2 | 2.4 | −0.5 | −0.7 | 1.2 | 1.0 | |
| Tubb6 | tubulin, beta 6 | 17 | 3 | 0.7 | 1.2 | 0.5 | −6.1 | −3.6 | 2.4 | 5.0 | −1.7 | 0.2 | 0.7 | |