Spreadsheet: 8c044c50-9365-48ca-b574-0a9fd682edd3
Sheet: Sheet1

Table S4
Figure 5A -Genes with Early, transient 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)
MT2370.3 |  | Rv2309A | 0.9707597 | 0.9840424 | 0.94395345 | 0.907164 | 0.89156836 | 0.89758974 | 0.92783964 | 0.9166955 | Hypothetical protein
MT3290.1 |  | whiB7;Rv3197A | 1.4549447 | 2.1729727 | 1.2925236 | 1.2032608 | 1.1391157 | 1.0619205 | 1.2679497 | 1.2034955 | conserved hypothetic
MT3290.2 |  |  | 1.5085682 | 2.2408338 | 1.4344695 | 1.1934496 | 1.248231 | 1.3605652 | 1.5281228 | 1.5742217 | hypothetical protein
MT3631 |  |  | 1.1400497 | 1.22431 | 1.0865172 | 1.0468109 | 1.0847598 | 1.0773492 | 1.11519 | 1.0894904 | hypothetical protein
Rv0022c | Rv0022c | whiB5;whmG | 1.4130348 | 1.4304287 | 1.173312 | 1.1758974 | 1.0738679 | 1.062202 | 1.1670234 | 1.2203861 | Rv0022c, (MTCY10H4.22c), unknown, len: 139, slight similarity to G466960 WHIB (102 aa) opt: 112, E(): 0.14, (34.3% identity in 67 aa overlap)
Rv0089 | Rv0089 |  | 1.2806048 | 1.4519225 | 1.2028587 | 1.1862704 | 1.0913584 | 1.1098386 | 1.0455458 | 1.1571662 | Rv0089, (MTCY251.07), len: 197. unknown, some similarity to sp|P12999|BIOC_ECOLI BIOTIN SYNTHESIS PROTEIN BIOC. (251 aa). FASTA scores: opt: 202 z-score: 262.0 E(): 4.5e-07; 39.0% identity in 118 aa overlap
Rv0090 | Rv0090 |  | 1.0019742 | 1.2530962 | 1.0493543 | 1.0215304 | 0.96835953 | 0.9802807 | 1.013817 | 0.9893554 | Rv0090, (MTCY251.08), len: 256. Unknown.
Rv0262c | Rv0262c | aac | 1.2375624 | 1.4761583 | 1.221565 | 1.1612155 | 1.1379739 | 1.1159363 | 1.0998424 | 1.1248139 | Rv0262c, (MTCY06A4.06c), len: 181 aa, highly similar to MFU41471_1 M. fortuitum [NAME] aminoglycoside 2'-N-acetyltransferase, (195 aa), [NAME] scores, opt: 884, E(): 0, (69.1% identity in 181 aa overlap). Also similar to MSU72743_1
[NAME] | [NAME] |  | 1.09121 | 1.173357 | 1.0787736 | 1.0306733 | 0.9699926 | 1.0496979 | 1.0174797 | 1.0355403 | [NAME], (MTCY25D10.39c), len: 271, methyl transferase, similar to eg Q54300 METHYLTRANSFERASE (211 aa), fastascores, opt: 203 z-score: 252.3 E(): 4.8e-07, (30.9% identity in 136 aa overlap)
Rv0887c | Rv0887c |  | 0.9191926 | 1.0423495 | 0.9005726 | 0.86911625 | 0.796526 | 0.83136505 | 0.86549294 | 0.90156305 | Rv0887c, (MTCY31.15c), len: 152, unknown
Rv0902c | Rv0902c | prrB | 1.1214507 | 1.3372939 | 1.2170838 | 1.1318779 | 1.0927912 | 1.0856946 | 1.1705936 | 1.0886627 | Rv0902c, (MTCY31.30c), len: 446. Probale two-component sensor similar to many sensor-like histidine kinase proteins e.g. CPXA_ECOLI P08336 sensor protein cpxa (457 aa),FASTA scores: opt: 364 z-score: 395.5 E(): 1.7e-15, 27.1%identity in 398 aa overlap
Rv1056 | Rv1056 |  | 1.0631269 | 1.1289594 | 1.0580267 | 0.97164255 | 1.0177226 | 0.96284467 | 1.0070038 | 1.0068281 | Rv1056, (MTV017.09), len: 254. Unknown but some similarity in C-terminal part to Mycobacterium tuberculosis MTCI5.14 (126aa). FASTA scores: Z92770|MTCI5_14 Mycobacteriumtuberculosis cosmid I (126 aa) opt: 254 z-score: 325.8 E(): 1.2e-10;43.4% identity in 106 aa overlap. TBparse scoreis0.925
Rv1200 | Rv1200 |  | 0.95138246 | 0.98835343 | 0.9322578 | 0.8962786 | 0.90294266 | 0.8956936 | 0.8978261 | 0.9457931 | Rv1200, (MTCI364.12), len: 425. Similar to e.g. YHJE_ECOLI P37643 hypothetical metabolite transport protein, (440 aa), [NAME] scores, opt: 1047 E(): 0, (39.1% identity in427 aa overlap); contains PS00217 Sugar transport proteinssignature 2
bcpB | Rv1608c |  | 1.009909 | 1.1570525 | 1.0660853 | 0.93677807 | 0.9289755 | 0.9007906 | 1.0243798 | 0.9170378 | Rv1608c, (MTV046.06), bcpB, len: 154. Probable bacterioferritin comigratory protein, similar to many, e.g. gp|AE0003|ECAE000335_4 E. coli K-12 MG1655 se (156 aa), FASTAscores: opt: 329 z-score: 433.7 E(): 1.2e-16; 38.2% identity in 152 aa overlap, or gp|Z97179|MLCL383_22 M. leprae cosmid L383. (161 aa), 40.2% identity in 132 aa overlap. Alsosimilar to MTV009_6 M. tuberculosis sequence (157 aa), 38.3% identity in 149 aa overlap
[NAME] | [NAME] |  | 1.1948876 | 1.2518278 | 1.1284493 | 1.0961158 | 1.0225433 | 1.0832685 | 1.0768722 | 1.0415455 | [NAME], (MTCY28.27c), len: 127. Unknown
Rv1926c | Rv1926c | mpt63;mpb63 | 1.3448339 | 1.6681955 | 1.335315 | 1.1414299 | 1.3617024 | 1.1284755 | 1.3640621 | 1.2669164 | Rv1926c, MTCY09F9.38, len: 159 aa. Unknown, probably exported protein contains N-terminal signal sequence.
Rv1988 | Rv1988 |  | 1.2095417 | 1.6350414 | 1.272924 | 1.1750327 | 1.1608412 | 1.0723592 | 1.0330302 | 1.1087614 | Rv1988, (MTCY39.31c), len: 179, methyltransferase, similar to eg ERME_SACER P07287 rrna adenine n-6-methyltransferase (370 aa) FASTA scores, opt: 259, z-score: 322.8, E(): 2e-11, (35.1% identity in 171 aa overlap); contains PS00092 [NAME] DNA methylases signature
Rv2050 | Rv2050 |  | 1.2215996 | 1.3170619 | 1.1884518 | 1.1017901 | 1.1658703 | 1.1031135 | 1.0969838 | 1.0753379 | Rv2050, (MTV018.37), len: 111. Unknown but similar to hypothetical protein Mycobacterium leprae MLCB2052.03c (113 aa). FASTA scores: Z98604|MLCB2052_3 Mycobacterium leprae cosmid B2052 (113 aa) opt: 737 z-score: 913.6 E(): 0;97.3% identity in 111 aa overlap. TBparse score is 0.884
panB | Rv2225 |  | 1.1046084 | 1.3041061 | 1.136229 | 1.0354271 | 1.0054793 | 0.9846984 | 1.0022986 | 0.92342293 | Rv2225, (MTCY427.06), len: 281. panB, similar to SW:PANB_ECOLI P31057 3-methyl-2-oxobutanoate hydroxymethyltransferase (45.9% identity in 257 aa overlap)
glpD1 | Rv2249c |  | 1.2877833 | 1.4145571 | 1.2197204 | 1.2051791 | 1.2222936 | 1.2522763 | 1.2319396 | 1.2213681 | Rv2249c, (MTCY427.31c), len: 516. [NAME], glycerol-3-phosphate dehydrogenase, similar to SW:GLPD_ECOLI P13035 aerobic glycerol-3-phosphate dehydrogenase (30.0% identity in 486 aa overlap) and SW:GLPA_ECOLI P13032 anaerobic glycerol-3-phosphate dehydrogenase (28.2% identity in 504 aa overlap)
Rv2269c | Rv2269c |  | 1.1773204 | 1.3745626 | 1.2070422 | 1.152784 | 1.1439594 | 1.1380935 | 1.1858761 | 1.1493276 | Rv2269c, (MTCY339.41), len: 110. Unknown, questionable orf
Rv2414c | Rv2414c |  | 0.987213 | 1.0585093 | 0.9098219 | 0.85369384 | 0.8671371 | 0.90737927 | 0.8761964 | 0.88785183 | Rv2414c, (MTCY253.06), len: 514. Unknown but similar to CME3_BACSU P39695 come operon protein 3 (776 aa), [NAME] scores, opt: 273, E(): 5.7e-10, (25.2% identity in 282 aaoverlap)
ahpD | Rv2429 |  | 1.353559 | 1.392494 | 1.1166993 | 1.0177072 | 1.0817041 | 0.9830486 | 1.1459756 | 1.1125629 | Rv2429, (MTCY428.17c), 177 aa. ahpD gene, identicalto G1174227 AHPD
Rv2559c | Rv2559c |  | 1.0942545 | 1.2397296 | 1.1489522 | 1.0544096 | 1.0773214 | 1.0340067 | 1.0640535 | 1.0341765 | Rv2559c, (MTCY9C4.09), len: 452. Similar to egYCAJ_HAEIN P45262 hypothetical protein hi1590. (446 aa) FASTA scores, opt: 1140, z-score: 1193.7, E(): 0, (42.5% identity in 428 aa overlap); contains PS00017 [NAME]/GTP-binding site motif A; also to [NAME], (30.1% identit in 296 aa overlapy
Rv2705c | Rv2705c |  | 1.4589903 | 1.6066947 | 1.4199651 | 1.3164057 | 1.3948398 | 1.3318219 | 1.380908 | 1.2645879 | Rv2705c, (MTCY05A6.26c), en: 129. Function: unknownunlikely orf
Rv3144c | Rv3144c | PPE52 | 1.0127766 | 1.2703305 | 1.0930512 | 1.0092515 | 0.94654983 | 0.9770219 | 1.0648139 | 0.9417101 | Rv3144c, (MTCY03A2.14), len: 409 aa. PPE family protein, Gly-, Ala-rich, similar to MTCY03C7.23, [NAME], MTCY6G11_5, MTCY98.0034c, MTCY31.06c, MTCY48.17, MTCY98.0029c, MTCY03C7.17c, etc. TBparse score is 0.891
Rv3258c | Rv3258c |  | 1.0992022 | 1.202067 | 1.0181947 | 0.9447286 | 0.96226335 | 1.0181638 | 1.0132378 | 0.9730916 | Rv3258c, (MTV015.03c), len: 163. Unknown. TBparse score is 0.928
[NAME] | [NAME] | PE_PGRS50 | 1.1795168 | 1.2600254 | 1.1341406 | 1.1290349 | 1.0811505 | 1.1125612 | 1.1559329 | 1.0880245 | Rv3345c, (MTV004.01c-MTV016.45c), member of the M. tuberculosis PE-PGRS family of Glycine-rich proteins, len 1538; similar to many eg. Y0DP_MYCTU Q50615 MTCY1A11.25Cc(498 aa), [NAME] scores; opt: 1646 z-score: 657.9 E(): 1.7e-29,55.0% identity in 565 aa overlap. Also similar to [NAME], MTV023_15, [NAME], MTV039_16, MTV008_46, MTV023_14, MTV023_19, MTV043_26, MTCY493_2, MTCY441_4 etc.
Rv3362c | Rv3362c |  | 1.1299585 | 1.3631821 | 0.9734437 | 0.94506055 | 0.9208781 | 0.94329983 | 0.86866736 | 0.82040673 | Rv3362c, ([NAME]), len: 193, unknown ATP/GTP binding protein, contains PS00017 [NAME]/GTP-binding site motif A (P-loop)
Rv3701c | Rv3701c |  | 0.954283 | 1.0469673 | 0.9758717 | 0.90770996 | 0.9258411 | 0.9491112 | 0.9619374 | 0.9237803 | Rv3701c, (MTV025.049c), len: 321. Unknown, but similar to hypothetical protein of Synechocystis sp. FASTA scores: gp|D90909|D90909_49 Synechocystis sp. PCC6803 complete(337 aa), opt: 779 z-score: 960.8 E(): 0; 40.4% identityin 327 aa overlap.
Rv3742c | Rv3742c |  | 1.0372547 | 1.6292363 | 1.1319244 | 0.95923275 | 1.0097939 | 1.0910565 | 1.0321307 | 0.9784735 | Rv3742c, (MTV025.090c), len: 131. Unknown but similar to the N-terminus of probable monooxygenase gp|Z83864|MTCY1A6_14 Mycobacterium tuberculosis cosmid (489 aa).FASTA scores: opt: 140 z-score: 188.1 E(): 0.0057. 37.1% identity in 132 aa overlap.or [NAME]. Also similar to L-LACTATE DEHYDROGENASES e.g. LDH_LACSK (325, 27.6% identity in 123aa overlap). Next ORF downstream (MTV025.089c) also showssimilarityto MTCY1A6_14 and [NAME] after a gap of 100 aa.TBparsescore is 0.915
Rv3822 | Rv3822 |  | 1.3997802 | 1.768082 | 1.3309832 | 1.2241877 | 1.2879028 | 1.1153946 | 1.1519527 | 1.1140466 | Rv3822, (MTCY409.08c), len: 404. Unknown, similar to M. leprae hypothetical protein Q49633 [NAME] (391 aa),fasta scores; opt: 601 z-score: 485.5 E(): 5e-20, 36.3% identity in 342 aa overlap. Also similar to M. tuberculosis hypothetical proteins e.g. MTCY03C7.17c (38.1% identity in 281 aa overlap). Alsosimilar to Rv1184c, Rv1430, Rv0159c etc.