Transcriptomic comparison of Aspergillus niger growing on two different sugars reveals coordinated regulation of the secretory pathway

Table 3 The 10, most highly and differentially expressed, secreted-carbohydrase genes on xylose or maltose.

ORF	gene name	encoded enzyme (homolog)	fold difference	signal xylose	SD	signal maltose	SD	p	FDR
High expression on maltose (maltose/xylose):
An03g06550	glaA	glucoamylase	3.5	4,175	574	*12,892	805	1.8·10^-8	4.5·10^-5
An04g06920	agdA	extracellular alpha-glucosidase	25.0	468	54	10,460	1,117	6.8·10^-12	8.5·10^-8
An11g03340	aamA	acid alpha-amylase	100.5	37	11	3,202	356	3.6·10^-10	1.1·10^-6
An09g00260	aglC	alpha-galactosidase	4.9	450	61	1,973	310	1.8·10^-8	1.4·10^-5
An12g08280	inu1	extracellular exo-inulinase	25.2	57	9	1,279	44	9.9·10^-10	2.4·10^-6
High expression on xylose (xylose/maltose):
An01g00780	xynB	endo-1,4-xylanase	22.3	7,846	1,169	422	346	1.5·10^-4	4.6·10^-3
An01g09960	xlnD	xylosidase	43.3	5,260	205	182	185	1.7·10^-4	5.1·10^-3
An14g02760	eglA	endo-glucanase	81.3	4,079	476	56	47	4.0·10^-7	1.1·10^-4
An14g05800	aguA	alpha-glucuronidase	45.0	3,619	433	81	45	1.4·10^-6	2.2·10^-4
An09g03300	axlA	alpha-xylosidase	10.3	3,365	529	438	398	2.5·10^-3	3.2·10^-2

ORF = identifier for open reading frame in A. niger CBS513.88 genome sequence [3]; gene name in A. niger; enzyme encoded by ORF (gene product and species name in parenthesis indicate closest ORF-homolog with characterized function); fold difference reflects ratio of normalized transcript levels (maltose/xylose or xylose/maltose); mean signal values of six experiments on each carbon source and standard deviations (SD) is given in Affymetix units; significance of each observation is given by p-value (p) and the Benjamini-Hochberg false discovery rate (FDR).
*signal of An03g06550-probeset appears saturated, leading to underestimation of glaA-transcription in maltose-limited chemostat cultures.

ISSN: 1471-2164