Table 3. Genes up-regulated in stationary phase in Cultures 1 and 2 and in further conditions in vitro or in vivo.

Gene ID (Rv no.)	Gene Name	Clusterno.	Function	Also up-regulated in the following studies:
Rv0083		2	Oxidoreductase	Human granuloma v in vitro culture in 7H9; [27]
Rv0122		2	Hypothetical protein	96h starvation in PBS [23]
Rv0251c	hsp	16	Heat shock protein	Human granuloma v in vitro [27] 96h starvation in PBS [23] 75 days starvation [10]
Rv0284		50	Conserved membrane protein	75 days starvation [10]
Rv1072		11	Conserved membrane protein	75 days starvation [10]
Rv1285	cysD	2	Sulfate adenylyltransferase	75 days starvation [10]
Rv1461		15	Conserved hypothetical protein	75 days starvation [10]
Rv1462		3	Conserved hypothetical protein	75 days starvation [10]
Rv2497c	pdhA	2	Pyruvate dehydrogenase	75 days starvation [10]
Rv2642		14	Transcriptional regulator, arsR	Human granuloma v in vitro culture in 7H9 [27]
Rv2710	sigB	16	RNA polymerase sigma factor	75 days starvation [10]
Rv3139	fadE24	3	Acyl-CoA dehydrogenase	75 days starvation [10]
Rv3173c		4	Transcriptional regulator, tetR acrR-family	75 days starvation [10]
Rv3555c		3	Conserved hypothetical protein	Human granuloma v in vitro culture in 7H9, Human granuloma v pericavity [27]

Table 3 Genes that were up-regulated at 48 h in macrophages [26] and in Cultures 1 and 2 of M. tuberculosis in late stationary phase (Table S3, supporting information), and in at least one other condition either in vitro or in vivo model as indicated in Table 3. The details of cluster profiles can be found in the supporting information at http://xenakis.mrc-bsu.cam.ac.uk/wernisch/enrichment/html/.