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.

Raman et al. BMC Systems Biology 2008 2:109   doi:10.1186/1752-0509-2-109

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