TABLE 2.

Comparison of the transcriptional responses by the wild type and the ccg-8 mutant to ketoconazole stress by gene set^a

Locus and/or categoryb	Gene	Function	TPM in WT	TPM in WT(k)	Fold change [WT(k)/WT]	P value	TPM in Δccg-8	TPM in Δccg-8(k)	Fold change [Δccg-8(k)/Δccg-8]	P value	Fold change [Δccg-8(k)/WT(k)]	Sensitivity to ketoconazole compared to WT's
Phospholipid synthesis pathways
NCU06666	ino1	Inositol-3-phosphate synthase	38.86	21.55	0.55	2.65E−05	180.9	17.25	0.09	4.7E−117	0.80	Similar
NCU08045	cho2	Phosphatidylethanolamine N-methyltransferase	11.22	6.16	0.55	0.022589	110	27.06	0.25	3.34E−41	4.39	NA
NCU03695	psd1	Phosphatidylserine decarboxylase proenzyme 1	28.78	51.28	1.78	1.87E−14	69.7	115.08	1.65	7.63E−10	2.26	Similar
NCU02381	cho1	Phosphatidylserine synthase	18.13	8.12	0.45	0.000217	29.96	13.08	0.44	1.91E−06	1.61	NA
NCU09643	cds1	Phosphatidate cytidylyltransferase	17.56	13.43	0.76	0.165267	24.02	18.73	0.78	0.138875	1.39	NA
Kinases participating in Opi1p (CCG-8 homolog in S. cerevisiae) phosphorylation
NCU06240	pkac-1	Catalytic subunit protein kinase A	26.48	24.63	0.93	0.6266	40.04	9.81	0.25	5.40E−16	0.40	Similar
NCU06544	pkc	Protein kinase C	24.75	67.16	2.71	0	52.79	24.98	0.47	5.28E−09	0.37	Similar
NCU03124	ck2	Catalytic subunit of protein kinase CK2	68.21	155.87	2.29	1.61E−13	52.2	60.07	1.15	0.173376	0.39	Similar
Target enzyme of azoles and multidrug transporters
NCU02624	erg11	Cytochrome P450 lanosterol 14a-demethylase	69.08	676.66	9.80	0	113.9	254.84	2.24	4.01E−13	0.38	NA
NCU05591	cdr4	ABC transporter CDR4	3.74	259.97	69.51	2.17E−07	4.75	54.42	11.46	4.10E−08	0.21	Hypersensitive
NCU04161		Multidrug resistance-associated protein 5	2.59	20.99	8.10	2.57E−06	4.75	6.84	1.44	0.264586	0.33	Similar
Stress responses
NCU01499		Related to hsp70	16.12	39.74	2.47	1.97E−09	35.29	147.49	4.18	0	3.71	Similar
NCU06317	kts-1	Stress response RCI peptide	123.19	1142.04	9.27	1.56E−13	323.3	412.45	1.28	1.56E−09	0.36	Hypersensitive
NCU09873	pck-1/acu-6	Phosphoenolpyruvate carboxykinase	4.89	31.06	6.35	1.68E−08	300.1	275.96	0.92	0.064493	8.88	Similar
NCU00355	cat-3	Catalase-3	135.85	252.42	1.86	0	54.28	24.98	0.46	1.08E−09	0.10	Similar
Transcription factors
NCU09686	ccg-8	Clock-controlled protein 8	33.97	127.89	3.76	3.94E−13	0	0				Hypersensitive
NCU01386	kts-2	Zn(II)2Cys6 domain-containing protein	0.58	26.86	46.31	0.000112	1.78	5.95	3.34	0.00582	0.22	Hypersensitive
NCU01629		C2H2 finger domain-containing protein	4.03	53.45	13.26	1.15E−07	28.77	25.57	0.89	0.427838	0.48	Similar
NCU05536		Zn(II)2Cys6 domain-containing protein	6.04	48.97	8.11	1.25E−09	6.23	8.33	1.34	0.317684	0.17	Similar
NCU09496		C2H2 transcription factor	10.07	97.94	9.73	2.66E−13	37.37	47.58	1.27	0.042249	0.49	NA
NCU04022		C2H2 finger domain-containing protein	12.66	120.89	9.55	6.62E−14	33.22	29.44	0.89	0.38236	0.24	NA
NCU09915	fsd-1/ndt80	Female sexual development-1 protein	7.77	46.17	5.94	2.51E−11	46.56	21.41	0.46	1.60E−08	0.46	Hypersensitive

^aWT, wild type; WT(k) or Δccg-8(k), wild type or Δccg-8 mutant treated with ketoconazole, respectively; TPM, number of locus tags per million; NA, the mutant was not available.

^bLocus numbers and function were annotated according to the N. crassa genome assembly (http://www.broadinstitute.org/annotation/genome/neurospora/).