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Table 2 Models and methods used in the targetTB pipeline

From: targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis

Analysis Coverage N/A ✔ X   Computation
(A) Systems Analysis       
   (i) Network 3405   431 2974   Single node deletions
   (ii) FBA       
a) Mtb iNJ 661 661   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   
  1. 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.
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