Spreadsheet: 5293e802-1ba2-4ddc-8b8c-4f10a1ce6a4c
Sheet: Sheet1

Table S10
Figure 5E - Genes with Delayed induced temporal profile
 |  |  | Time
 |  |  | 2hr | Day 2 | Day 4 | Day 6 | Day 8 | Day 10 | Day 12 | Day 14
Gene | Common | Synonym | Ratio | Ratio | Ratio | Ratio | Ratio | Ratio | Ratio | Ratio | Description (Tuberculist annotation)
MT0768.1 |  |  | 0.8548368 | 1.0947106 | 1.2200803 | 1.2729914 | 1.2803935 | 1.1812345 | 1.2036602 | 1.0577341 | Hypothetical protein
MT2015.1 |  |  | 0.91951025 | 1.117551 | 1.2405598 | 1.3055195 | 1.3777134 | 1.1960235 | 1.1871501 | 1.0253178 | hypothetical protein
[NAME] |  |  | 0.8785651 | 0.88649046 | 1.015276 | 1.0671134 | 1.0772362 | 1.035323 | 1.0335203 | 1.0081177 | hypothetical protein
MT3103 |  |  | 0.9685932 | 1.3653365 | 1.4434888 | 1.7784475 | 1.815892 | 1.6378044 | 1.487957 | 1.5968087 | hypothetical protein
Rv0326 | Rv0326 |  | 1.0022469 | 1.2473488 | 1.4721825 | 1.6840454 | 1.62467 | 1.4619644 | 1.4818134 | 1.4397056 | Rv0326, (MTCY63.31), len: 151. Function: unknown. TBparse score is 0.929
Rv0493c | Rv0493c |  | 1.2527701 | 1.8231797 | 1.8956304 | 2.1844077 | 2.3920913 | 2.4289026 | 1.9029526 | 1.8122064 | Rv0493c, (MTCY20G9.19), len: 329, unknown, some similarity to U00018_33 Mycobacterium leprae cosmid B2168 B2168_F2_93 (167 aa) FASTA scores, opt: 166, z-score: 193.6, E(): 0.00077, (35.9% identity in 131 aa overlap)
Rv0514 | Rv0514 |  | 0.74198216 | 0.864592 | 0.9128359 | 0.97547084 | 1.003212 | 0.9798147 | 0.9481347 | 0.91561407 | Rv0514, (MTCY20G10.04), len: 99, unknown, possible membrane protein
Rv0538 | Rv0538 |  | 0.8777102 | 0.98851097 | 1.0666335 | 1.131166 | 1.1547029 | 1.0899976 | 1.0367941 | 1.083983 | Rv0538, (MTCY25D10.17), len: 748, unknown, partially identical to AF009829_1 Mycobacterium bovis [NAME] O32850, possible transmembrane protein with a repetitive proline, threonine-rich region at c-terminus
fadE9 | Rv0752c |  | 0.95191854 | 0.87586844 | 1.2515045 | 1.3898581 | 1.4162236 | 1.3596141 | 1.2578001 | 1.2958874 | Rv0752c, (MTV041.26c), len: 390, acd , fadE9, probable acyl-CoA dehydrogenase, ,similar to many other acyl-CoA dehydrogenases e.g. [NAME] subtilis complete genome (379 aa) FASTA scores: opt: 853 z-score: 958.3 E(): 0. 39.8% identity in 384 aa overlap. Contains PS00072 Acyl-CoA dehydrogenases signature 1 and PS00073 Acyl-CoA dehydrogenases signature 2
[NAME] | Rv0753c |  | 0.9766579 | 1.1604983 | 1.4424728 | 1.5803107 | 1.673945 | 1.5436844 | 1.3015519 | 1.2799734 | Rv0753c, (MTV041.27c), len: 510. [NAME], probable methylmalonate semialdehyde dehydrogenase, ([NAME]), similar to many e.g. gp|M84911|PSEMMSRAB_2 Pseudomonas aeruginosa methylmal (497 aa).opt: 1127 z-score: 1345.6 E(): 0; 47.9% identity in 507 aa overlap, or gp|L48550|STMMSDA_1 Streptomyces coelicolor methylmalo (500 aa), 51.6% identity in 498 aa overlap. Contains PS00070 [NAME] dehydrogenases cysteine active site
Rv0754 | Rv0754 | PE_PGRS11 | 0.85901237 | 1.1864479 | 1.3129107 | 1.4979119 | 1.5242091 | 1.4086621 | 1.1544323 | 1.2287123 | Rv0754, (MTV041.28), len: 584. Unknown glycine richprotein, similar to other PE_PGRS type hypothetical proteins e.g. gp|AL0212|MTV008_46 M. tuberculosis sequenc (1660 aa); 48.7% identity in 345 aa overlap or gp|Z80225|MTCY441_4M. tuberculosis cosmid (778 aa); 41.6% identity in 442 aaoverlap
Rv0762c | Rv0762c |  | 0.9806483 | 1.037205 | 1.1930717 | 1.2030488 | 1.1832029 | 1.1497492 | 1.1334028 | 1.1056933 | Rv0762c, (MTCY369.07c), len: 181; unknown, weak similarity to D90907_77 Synechocystis P73575 HYPOTHETICAL 31.3KD PROTEIN, E(): 0.0012, 30.4% identity in 92 aa overlap. contains PS00017 [NAME]/GTP-binding site motif A
[NAME] | [NAME] | cyp51 | 0.95910543 | 1.0670391 | 1.2009873 | 1.2218904 | 1.228354 | 1.1940018 | 1.1224214 | 1.0756177 | [NAME], (MTCY369.09c), len: 451, similar to eg sp|Q16850|CP51_HUMAN CYTOCHROME P450 L1 (LANOSTEROL 14 (509 aa), opt: 848 z-score: 996.6 E(): 0; 33.9% identity in 439 aa overlap; contains PS00086 Cytochrome P450 cysteine heme-iron ligand signature; also similar to MTCY21B4.11c (22.5% identity in 444 aa overlap)
Rv0765c | Rv0765c |  | 1.0799079 | 1.4187185 | 1.5460664 | 1.6847733 | 1.5940065 | 1.6199374 | 1.4391367 | 1.445035 | Rv0765c, ([NAME]), len: 275, probable OXIDOREDUCTASE, similar eg to DHBA_BACSU P39071 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (261 aa), [NAME] scores, opt: 385, E(): 1.8e-17, (30.6% identity in 252 aa overlap); contains PS00061 Short-chain alcohol dehydrogenase family signature; similar to several other [NAME] genes eg MTCY48.21 (32.6%identity in 267 aa overlap)
Rv0828c | Rv0828c |  | 0.8245874 | 0.82852584 | 0.9481179 | 1.0102392 | 1.0428452 | 0.9539909 | 0.8772408 | 0.89932525 | Rv0828c, (MTV043.20c), len: 140. Unknown but similar in part to [NAME] YKOA (156 aa), E(): 1.3e-07, (38.9% identity in 95 aa overlap) and to Bradyrhizobium japonicum nitrogen fixation protein gene gp|L34743|RHBNFXP_1 B. japonicum nitrogen (142 aa); 50.0% identity in 44 aa overlap.. Contains PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature
Rv0870c | Rv0870c |  | 0.9846403 | 1.1247834 | 1.2286518 | 1.3575733 | 1.3770719 | 1.2512698 | 1.2255477 | 1.1788508 | [NAME], (MTV043.63c), len: 129. Unknown hydrophobic proetin, similar to HYPOTHETICAL 16.3 KD E. COLI PROTEIN P37065|YCCF_ECOLI(148 aa). FASTA scores: sp|P37065|YCCF_ECOLI HYPOTHETICAL 16.3 KD PROTEIN (148 aa) opt: 183 z-score:250.5 E(): 1.9e-06; 36.6% identity in 134 aa overlap. TBparse score is 0.886
Rv1004c | Rv1004c |  | 0.824722 | 0.8142768 | 0.8859298 | 0.9437844 | 0.8984581 | 0.9245578 | 0.86960125 | 0.8573591 | Rv1004c, ([NAME]), len: 419. Contains repetitive sequence, which has similarities with elastin, and possible N-terminal signal sequence
Rv1087 | Rv1087 | PE_PGRS21 | 0.9086974 | 1.1332462 | 1.1955096 | 1.2894301 | 1.2137231 | 1.2707964 | 1.157133 | 1.111778 | Rv1087, (MTV017.40), len: 767. Member of M. tuberculosis PE family, Gly-, Ala-rich PGRS subfamily. Contains PS00583 [NAME] of carbohydrate kinases signature 1 near C-terminus.FASTA scores: sp|P71933|YQ04_MYCTU HYPOTHETICAL 63.1 KD GLYCINE-RICH (778 aa) opt: 2365 z-score: 1413.2 E(): 0; 53.5% identity in 809 aa overlap. TBparse score is0.859
Rv1222 | Rv1222 |  | 0.97265047 | 1.2239426 | 1.3033534 | 1.3588333 | 1.4067211 | 1.2887133 | 1.2405072 | 1.2417406 | Rv1222, (MTCI61.05), len: 154. Identical to, but shorter than PID:g2062625 from EMBL:MTU87242, due to different start site chosen by proximity of RBS
Rv1895 | Rv1895 |  | 0.9750543 | 1.0082152 | 1.173291 | 1.1849436 | 1.1533246 | 1.1185403 | 1.1587276 | 1.0973058 | Rv1895, ([NAME]), len: 384; similar to varioussorbitol and alcohol dehydrogenases. FASTA results: [NAME] Q06004 sorbitol dehydrogenase (ec 1.1.1.14) (352 aa) opt: 506; E(): 7.2e-24; 30.6% identity in 350 aa overlap. Note that there is a substantial (134bp) overlap at the C-terminus with the C-terminus of the downstream ORF, although both appear to be true coding regions. TBparse score is 0.922. Also similar to other M. tuberculosis dehydrogenases
Rv1936 | Rv1936 |  | 0.9543634 | 1.370746 | 1.7669466 | 2.101917 | 2.1596336 | 1.8333124 | 1.6137592 | 1.3883524 | Rv1936, (MTCY09F9.28c), len: 369 aa. Similar eg to LXA2_PHOLU P23146 alkanal monooxygenase alpha chain (362 aa), [NAME] scores, opt: 196, E(): 6.3e-06, (22.3% identity in373 aa overlap)
Rv1952 | Rv1952 |  | 1.1077386 | 1.1138623 | 1.2489909 | 1.265207 | 1.2842592 | 1.1971767 | 1.1672896 | 1.1503848 | Rv1952, (MTCY09F9.12c), len: 71 aa. Some similarityto P55510|Y4JJ_RHISN PUTATIVE PLASMID STABILITY PROTEI (85aa) FASTA scores: opt: 127 z-score: 202.3 E(): 0.00096; 42.5% identity in 73 aa overlap
Rv2516c | Rv2516c |  | 0.88920426 | 0.9781978 | 1.0954809 | 1.1730701 | 1.1678555 | 1.144505 | 1.0293463 | 1.1128459 | Rv2516c, (MTV009.01c), len: 249. Unknown; Contains probable helix-turn-helix motif at aa 99 to 120 (Score 1641, [NAME]). TBparse score is 0.964
Rv2618 | Rv2618 |  | 0.8690885 | 1.033764 | 1.122886 | 1.2230815 | 1.2906847 | 1.142103 | 1.0433658 | 1.1035079 | Rv2618, (MTCY01A10.15c), len: 225 aa. Unknown, somesimilarity to MTCY01A10.11, (224 aa) opt: 149 z-score: 157.6 E(): 0.0013, (28.9% identity in 197 aa overlap) and othermycobacterial proteins
Rv2662 | Rv2662 |  | 0.975999 | 1.2065368 | 1.4711881 | 1.6296127 | 1.613213 | 1.6178725 | 1.2242546 | 1.3732774 | Rv2662, (MTCY441.31), len: 90. Unknown
Rv2695 | Rv2695 |  | 0.86465156 | 1.0392802 | 1.2090194 | 1.269071 | 1.2918316 | 1.0809261 | 1.0896547 | 1.0607392 | Rv2695, (MTCY05A6.16), len: 235. Function: unknown very similar to hypothetical M. leprae protein, U1764L. FASTA best: G699170 U1764L opt: 1123; E(): 0; 82% identity in 231 aa overlap. TBparse score is 0.897
Rv2742c | Rv2742c |  | 0.9538574 | 1.0594778 | 1.0761491 | 1.2800465 | 1.3867259 | 1.2495637 | 1.1260424 | 1.1539539 | Rv2742c, (MTV002.07c), len: 277 aa. Questionable ORF, extreme N-terminus is highly similar to the N-teminus ofthe downstream ORF MTV002.03c (78.4% identity in 37 aa overlap)
leuC | Rv2988c |  | 1.0465761 | 1.0231615 | 1.3269354 | 1.4826521 | 1.5172778 | 1.3985071 | 1.3415754 | 1.3522352 | Rv2988c, (MTV012.02c), len: 473. leuC, 3-isopropylmalate dehydratase large subunit, similar to many e.g. A.teichomyceticus leuC (X84647) best with M. leprae (Z99263|MLCB637_32). FASTA score: gp|Z99263|MLCB637_32 Mycobacterium leprae cosmid B637. (476 aa) opt: 2818 z-score: 3311.6 E(): 0; (88.7% identity in 471 aa overlap) and gp|X84647|ATLEUCD_1 A.teichomyceticus leuC and [NAME] (485 aa) opt: 1958 z-score: 2301.7 E(): 0; (71.0% identity in 479 aa overlap). Contains PS00450 Aconitase family signature. TBparse score is 0.895
Rv2989 | Rv2989 |  | 1.075915 | 1.249459 | 1.6299891 | 1.9064726 | 1.8903253 | 1.7806718 | 1.5709665 | 1.4428126 | Rv2989, (MTV012.03), len: 233. Unknown regulator, similar to several putative M. tuberculosis regulatory proteins e.g. [NAME] (248 aa), and to others e.g. to the IclRtype regulator, HppR, from Rhodococcus globerulus. Has potential helix-turn-helix motif at positions 26-47. FASTA score: gp|Z95890|MTCY28_39 Mycobacterium tuberculosis (248 aa)opt: 239 z-score: 301.9 E(): 2.5e-09; (29.9% identity in 231 aa overlap) and gp|U89712|RGU89712_5 Rhodococcus globerulus hpp operon (206 aa) opt: 203 z-score: 258.9 E(): 6.2e-07; (31.0% identity in 184 aa overlap). TBparse score is 0.894
Rv3230c | Rv3230c |  | 1.0754273 | 1.314836 | 1.4198833 | 1.4707947 | 1.4883345 | 1.3527364 | 1.3450222 | 1.2741882 | Rv3230c, (MTCY20B11.05c), len: 380. Function: unknown but some similarity to various oxygenases and reductase.FASTA scores: : Q44253 ANILINE DIOXYGENASE REDUCTASE COMPONENT.(336 aa) opt: 305 z-score: 352.8 E(): 1.2e-12; (27.4% identity in 303 aa overlap)
Rv3338 | Rv3338 |  | 0.976133 | 1.2293775 | 1.4208374 | 1.5984403 | 1.5750273 | 1.4149323 | 1.2760221 | 1.1883129 | Rv3338, (MTV016.38), len: 214. Unknown but similar to C-terminal part of hypothetical M. leprae protein MLCB1779.02 (292 aa). Homology suggests that this orf should be in frame with the previous one MTV016.37 but no sequence error could be found. FASTA scores: Z98271|MLCB1779_2 (292 aa) opt: 989 z-score: 1213.4 E(): 0; 62.4% identity in 229 aa overlap. Also similar to U00022_29 Mycobacterium leprae cosmid L308. 65.4% identity in 214 aa overlap. TBparse score is 0.887
Rv3408 | Rv3408 |  | 0.94719905 | 1.107145 | 1.3054943 | 1.3941113 | 1.4602972 | 1.2797742 | 1.2881824 | 1.2992433 | Rv3408, (MTCY78.20c), len: 136, unknown, but similar to MTV004_40 Mycobacterium tuberculosis (130 aa, E(): 1e-10, 35.1% identity in 131 aa overlap), MTCY09F9.02, MTV014_24
Rv3444c | Rv3444c | esxT | 0.8249521 | 0.8781841 | 0.9908029 | 1.0613929 | 1.1027082 | 1.021553 | 0.971238 | 1.0362905 | Rv3444c, (MTCY77.16c), len: 100 aa. Unknown but highly similar to Q49852 B229_C1_150 (49 aa) in C-terminus; [NAME] scores, opt: 227, E(): 8.3e-08, (68.9% identity in 45 aa overlap). Some similarity to [NAME]