Table 1. Fold-change and probe counts for selected A. fumigatus genes during growth in Aspergillus minimal medium (AMM) and during invasive growth in the mouse lung on days 2, 4, and 5.

				Fold-change relative to growth in AMM			Normalized Probe Counts
Process	Gene ID	Gene Name	Function	Day 2	Day 4	Day 5	AMM	Day 2	Day 4	Day 5
Iron homeostasis
	Afu1g17270	fre2	Metalloreductase involved in response to iron starvation	1.09	23.14	21.64	232	253	5369	5019
	Afu5g03920	hapX	bZIP transcription factor required for adaption to both iron depletion and excess and for transcriptional activation of the siderophore system	1.18	4.19	3.51	948	1123	3974	3326
	Afu2g07680	sidA	L-ornithine N5-oxygenase; first committed step in siderophore biosynthesis	3.06	10.93	9.07	9646	29495	105444	87529
	Afu3g03420	sidD	Nonribosomal peptide synthetase 4; involved in extracellular siderophore biosynthesis	4.98	15.17	17.36	1000	4981	15166	17351
	Afu3g03640	mirB	Putative siderophore iron transporter	5.27	31.94	22.07	1231	6480	39307	27157
	Afu7g06060	sit1	Putative siderophore transporter	0.44	10.50	6.88	1126	498	11822	7751
	Afu5g11260	sreA	GATA transcription factor that regulates iron uptake	0.00	0.14	0.08	2310	0	316	177
Zinc homeostasis
	Afu4g09560	zrfC	Zinc transporter that functions in neutral or alkaline environments	58.86	158.24	143.41	248	14598	39244	35566
	Afu1g01550	zrfA	Putative plasma membrane zinc transporter	18.82	10.41	8.15	19	354	196	153
	Afu4g09580	aspf2	Allergen Asp f 2; expressed in alkaline zinc-limiting conditions	47.91	218.08	136.52	170	8141	37057	23198
	Afu1g10080	zafA	Putative C2H2 zinc-responsive transcriptional activator	3.99	2.06	2.40	1010	4034	2084	2429
Nitrogen uptake
	Afu1g17470	nrtB	Putative high-affinity nitrate transporter	461.99	16.95	32.20	13	6162	226	429
	Afu6g01970	areA	Putative GATA-like transcription factor; required for growth on numerous nitrogen sources	0.00	1.71	2.08	1891	0	3234	3934
	Afu5g00710		GABA permease	9.63	45.45	39.14	168	1616	7633	6572
Stress response
	Afu2g01260	srbA	Sterol regulatory element binding protein (SREBP); basic helix-loop-helix leucine zipper DNA binding domain	0.85	1.81	1.73	9403	7991	16995	16299
	Afu3g04070	hacA	bZIP transcription factor, major regulator of the unfolded protein response	0.54	0.46	0.46	12752	6930	5895	5926
	Afu3g11970	pacC	C2H2 finger domain transcription factor; required for response to alkaline pH	0.59	1.73	1.72	1864	1100	3230	3202
	Afu4g09080	sebA	Putative transcription factor; localizes to the nucleus in response to oxidative stress and heat shock	4.56	6.42	5.33	868	3959	5571	4623
	Afu1g05800	mkk2	Putative mitogen-activated protein kinase kinase; essential for cell wall integrity signaling	0.11	2.91	2.62	1600	175	4662	4193
	Afu5g08420	sho1	Putative transmembrane osmosensor	0.44	2.30	2.42	2990	1309	6864	7233
	Afu5g04170	hsp90	Heat shock protein; allergen Asp f 12;	0.01	0.18	0.19	7795	90	1406	1518
	Afu8g01670	cat2	Putative bifunctional catalase-peroxidase	0.22	0.45	0.22	1450	319	655	312
	Afu4g11580	sod2	Putative manganese-superoxide dismutase	0.10	0.20	0.23	932	90	185	211
	Afu4g00860	dprA	Dehydrin-like protein; plays a role in oxidative, osmotic and pH stress responses	0.43	0.50	0.44	210	90	105	92
Secondary metabolite production
	Afu6g09690	gliG	Glutathione S-transferase encoded in the gliotoxin biosynthetic gene cluster	5469.48	6614.27	9370.72	0	882	1066	1510
	Afu6g09660	gliP	Non-ribosomal peptide synthetase encoded in the gliotoxin biosynthetic gene cluster	805.63	649.15	657.75	47	38108	30706	31113
	Afu6g09630	gliZ	Zn2Cys6 binuclear transcription factor, regulates genes required for gliotoxin biosynthesis	31.18	50.79	39.87	114	3552	5786	4542
	Afu6g02690	mtfA	Transcription factor involved in regulation of morphogenesis, gliotoxin production and virulence	2.47	8.05	9.08	351	867	2822	3184
	Afu7g00130	nscR	Pathway-specific Zn(II)2Cys6 transcriptional factor; role in neosartoricin and fumicycline A biosynthesis	21.31	209.35	308.36	12	263	2582	3803
	Afu3g00590	aspHS	Asp-hemolysin; hemolytic toxin	26.33	0.15	4.07	103	2707	15	419
	Afu5g02330	aspf1	Allergen Asp f 1; ribonuclease mitogillin family of cytotoxins	0.00	0.01	0.00	99853	468	951	320
	Afu8g00420	fumR	C6 zinc finger domain protein required for expression of fumagillin and pseurotin gene clusters	0.10	0.15	0.12	2416	237	365	290
	Afu3g12890	hasA	C6 transcription factor; hexadehydroastechrome biosynthesis	0.00	0.21	0.15	8234	0	1712	1231
	Afu4g14540	tpcE	Putative Zn2Cys6 transcription factor involved in trypacidin biosynthesis	0.00	0.23	0.16	172	0	40	27