Table 2.

Zone	Gene Clusters	Representative Gene Class
1	(CYSH Rv1478 GGTB NIRA Rv2425C ACCD4 Rv3541C Rv0175 Rv2393 MURX Rv3701C) (PNTAB KASA HEMC LPQI ACCD6 KASB Rv2052C Rv1728C ARGH)	Intermediate and lipid metabolism
2	(DRRB Rv1251C EFPA Rv2054 MURC Rv1632C Rv2395 Rv1378C QCRA CTAE RHO PARB Rv3321C ATPH Rv3921C ATPD Rv3805C Rv2901C PARA Rv2949C CTAC Rv1576C ATPB Rv0546C Rv2781C Rv0526 Rv3104C POLA PYRH Rv1870C Rv1711 Rv3672C Rv0514 DAPF Rv2554C Rv1869C NUOE NUOC Rv1178 Rv0528 Rv1481 Rv2791C Rv2610C Rv3856C Rv1565C Rv3212 Rv1043C TSNR Rv1324 PGK Rv0525 RUVC KSGA Rv2989 LPRE PURK Rv0412C RODA Rv3725 HEME Rv1339 Rv1797 NRP UREC Rv2852C Rv3781 TRPA Rv2956 TRPB Rv2808 Rv2128 Rv1695 NUOI Rv1312 NUOL NUOD Rv3806C Rv2759C Rv2966C FOLK Rv2879C Rv1780 Rv1271C Rv3693 PLCB DRRC Rv2600 NUOM NUOH Rv0875C Rv3220C Rv3885C MMPL7 Rv2475C LTP1 Rv0236C NUOJ NUOB NUON MMPL9 Rv2752C Rv0177 Rv0176 HEMB PRCA Rv2553C Rv2367C RPLT GID CMK Rv3122 EMBB Rv1303 Rv1907C Rv2792C)	Energy production and respiration
3	(FTSZ WAG31 Rv0902C HEMK NARL Rv2147C Rv3267 Rv1477 LPPW SIGC Rv2864C RECA Rv2826C Rv1697 LEUC LEUD Rv3909 DNAQ Rv1465 Rv0486 Rv3910 PIRG Rv2574 Rv2360C Rv3816C AROB Rv2827C FTSK Rv3587C FOLE FTSQ Rv3647C Rv3376 RHLE) (LEUA AMIC RPOA RPSE RPLF RPSH RPLX Rv0203 RPLJ RPLR RPLE RPLB RPLC NUSG) (RPSS ALR RPSC RPLV PNTB RPLP RPMC Rv2125 PRFA Rv1546 Rv3278C Rv1099C RPLO TPI Rv0299 Rv3677C Rv2258C) (RIMM Rv1258C RPLL Rv2908C RPLI Rv2822C PCKA Rv1073 Rv0636 Rv0637 CYSA2 Rv0277C RPSP RPSB LPPU HTPG RPLM RPSI SSEC2 Rv0057 SSB ASPC)	Information pathways (replication, transcription, and translation)
4	(SIGE Rv0516C Rv0846C Rv0991C Rv3334 Rv2628 Rv2020C Rv0968 Rv2517C NARK2 FBPC LPQS Rv2662 Rv1772 Rv0967 Rv0465C Rv1813C Rv2016 HSP Rv1847 Rv0190 Rv1774 RPST ALD Rv0080 Rv2699C Rv2629 Rv0571C Rv2623 Rv0572C Rv2005C CTPF Rv3133C Rv2004C Rv2626C Rv2625C Rv2627C Rv2032 PANB Rv2466C Rv2035 Rv3134C Rv2962C Rv0081 Rv2630) (WHIB4 Rv2668 Rv1136 Rv3342 Rv1234 PGMA Rv3895C Rv0941C LPPJ Rv0653C Rv3479 Rv1179C Rv2478C Rv0108C Rv2184C PDXH Rv0502 CDH Rv1352 FABG3 Rv3123 Rv1453 THYA LIPH Rv1893 Rv0650 ECHA14 Rv0771 Rv1413 Rv0121C Rv3654C Rv2044C LIPF Rv2670C CPSY Rv2297 Rv0165C PKS11 Rv1362C Rv2799 Rv1363C Rv2255C Rv1931C Rv3501C VIUB APT Rv1861 SECG Rv3860 Rv0149 Rv0269C Rv2639C Rv1151C Rv0230C MOAC3 Rv2722 TRXA Rv3891C Rv0188 Rv1535 Rv2288 Rv2657C Rv3764C Rv1230C Rv3288C LPQH Rv0695 Rv3633 Rv3616C Rv3399 LPRF Rv2638 Rv3615C Rv3614C PAPA3 FRDC Rv2129C Rv1926C SODA Rv2633C Rv2557 LAT Rv3733C Rv2161C PKS4 Rv2558 Rv2632C PKS3 Rv1868 NARG Rv3751 Rv0696 SIGF Rv3679 Rv2160C RSBW Rv2253 Rv2336 FUSA2 PAPA1 Rv2598 RELA PKS2 Rv3241C Rv1639C SUHB Rv1871C Rv3500C EPHA Rv1184C Rv0387C Rv1433 OMPA Rv0171 Rv3496C CDD MOAE2 Rv2024C FADE26 SCOA Rv0657C AMT Rv2348C Rv3750C Rv3491 Rv0137C Rv3887C Rv1037C Rv3874 Rv2137C LLDD2 Rv2311 Rv2205C NARJ NARH Rv2369C Rv0621 Rv1398C FURA Rv1154C Rv2472 Rv3449 FADD16 LPQO Rv0168 Rv0767C Rv0736 INFC FRDB Rv0245 NARI Rv0167 RIBC Rv0258C Rv2765 Rv1425 Rv1968) (PDHA Rv3802C LPPD GUAB1 Rv1783 Rv1782 Rv0126 GLYS Rv1892 Rv1978 Rv0654 Rv1885C Rv0760C Rv3850 OBG FBPB PRA Rv2958C NRDE Rv1956 Rv0192 Rv1988)	Cell wall, cell processes, and metabolism

The whole-genome gene expression image (Figure 1) was divided into four zones, each annotated with major gene clusters therein and the functional classes of representative genes. The list of genes in each zone is available [see Additional file 5].