Optimization of cDNA microarrays procedures using criteria that do not rely on external standards

BMC Genomics

Table 1 Selected GO categories associated with genes differentially expressed in the cell lines AR42J versus NRK52E.

GO number	GO term	A	B	AUB	BÚA	Proportion
GO:0008150	biological process	724	233	233	491	3.1
GO:0008152	metabolic process	459	135	135	324	3.4
GO:0032502	developmental process	246	91	91	155	2.7
GO:0007154	cell communication	202	69	69	133	2.9
GO:0050896	response to stimulus	165	64	64	101	2.6
GO:0048468	cell development	112	38	38	74	2.9
GO:0006950	response to stress	101	32	32	69	3.2
GO:0009056	catabolic process	65	30	30	35	2.2
GO:0007049	cell cycle	60	13	13	47	4.6
GO:0016265	death	60	18	18	42	3.3
GO:0006928	cell motility	51	17	17	34	3.0
GO:0040007	growth	42	19	19	23	2.2
GO:0006952	defence response	32	7	7	25	4.6
GO:0019725	cell homeostasis	30	12	12	18	2.5

A: Gene list generated with no background correction and weight based filtering. B: Gene list generated with dampened Edwards background correction and weight based filtering. AUB: number of genes differentially expressed in both gene list A and B. AÚB: number of genes differentially expressed in gene list A but not in gene list B. BÚA: number of genes differentially expressed in gene list B but not in gene list A. Proportion: number of genes in A/number of genes in B. The genes were annotated using GeneTools [30] according to UniGen build #163. All GO categories associated with more than five genes are shown in Additional file 2.

ISSN: 1471-2164