Table 2.
Models and methods used in the targetTB pipeline
| Analysis | Coverage | N/A | ✔ | X | Computation | |
| (A) Systems Analysis | ||||||
| (i) Network | 3405 | 431 | 2974 | Single node deletions | ||
| (ii) FBA | ||||||
| a) Mtb iNJ661 | 661 | 229 | 432 | FBA | ||
| b) GSMN-TB | 717 | 259 | 458 | FBA | ||
| c) MAP | 26 | 15 | 11 | FBA | ||
| (iii) TraSH | 3186 | 656 | 2530 | |||
| Summary ((i) or (ii) or (iii)) | 3823 | 166 (A') | 1138 | 2685 | (AX) | |
| (B) Sequence Analysis | 3989 | 3611 | 378 | (BX) | 3,989 Mtb vs. 33,453 human sequence comparisons | |
| (A&B) Systems & Sequence Passed | 3989 | - | 942 | 3047 | (AX∪ BX) | |
| (C) Structural Assessment (PMScore < 0:8) [942 from A&B only considered] | 767 | 175 (C') | 622 | 145 | (CX) | 3,500 sites of Mtb (767 proteins) vs 70,149 sites of Human pocketome (15,830 proteins) = 245,521,500 pairwise comparisons |
| (D) A & B & C | 3989 | - | 622 | 3552 | (AX∪ BX∪ CX∪ C') | |
| (E) Expression | ||||||
| (i) Gao-expression | 3590 | 399 | 2210 | 1380 | ||
| (ii) Rachman-expression | 634 | 3355 | 634 | - | ||
| (iii) Boshoff-expression | 3915 | 74 | 3915 | - | ||
| Summary ((i) or (ii) or (iii)) | 3917 | 72 | 3264 | 653 | (EX) | |
| Summary (for (D)) | 622 | 1 | 529 | 92 | ||
| (F) Non-similarity to Anti-targets | 3989 | - | 3928 | 61 | (FX) | 306 vs. 3,989 sequence comparisons |
| Non-similarity to Anti-targets (for (D)) | 622 | - | 611 | 11 | ||
| (G) Non-similarity to gut flora | 3989 | - | 3730 | 259 | (GX) | 296,017 vs. 3,989 sequence comparisons |
| Non-similarity to gut flora (for (D)) | 622 | - | 543 | 79 | ||
| (H) D & E & F &; G | 622 | 1 | 451 | 170 | ||
| (I) Expression during Persistence | ||||||
| (i) Muttucumaru-expression | 3924 | 82 | 639 | 3268 | ||
| (ii) Boshoff-expression | 3915 | 74 | 105 | 3810 | ||
| (iii) Betts-expression | 3649 | 340 | 274 | 3375 | ||
| (iv) Voskuil-expression | 3924 | 82 | 310 | 3597 | ||
| (v) Hampshire-expression | 3757 | 395 | 1349 | 2245 | ||
| Summary ((i) or (ii) or (iii) or (iv) or (v)) | 3933 | 73 | 1871 | 2045 | ||
| Summary (for (H)) | 451 | - | 216 | 235 | ||
| (J) Broad-spectrum Targets [present in > 100/228 pathogenic genomes] | 451 | - | 186 | 265 | 2,295,901 vs. 3,989 sequence comparisons (phylo-Genetic profiling against 707 genomes) | |
| (K) Targets unique to Mycobacteria | 451 | - | 66 | 385 | ||
Number of proteins covered in each study are indicated. A '✔' indicates that it passes the filter, while a 'X' indicates failure. The method used at each step is also indicated. The number of targets identified in the final lists H, I, J and K are boxed and indicated in bold typeface. The symbols A', C', AX-GX are as described in the text and in Fig. 1.