Characterizing the stress/defense transcriptome of Arabidopsis

Table 4 Comparison of the present stress-inducible cDNA collection with stress/defense genes identified in other large-scale studies

Study	Cut-off	Induced/repressed clones	MIPS id	Represented in stress cDNA collection	Treatment
[7]	2.5-fold	413	308	50 (16%)	Benzothiadiazol treatment, bacterial and oomycete pathogen
[17]	2.5-fold	705	507	160 (32%)	Fungal pathogen, SA, MJ, ethylene
[48]	2-fold	657	281	73 (26%)	Mechanical wounding
[18]	1.5-fold	175	114	32 (28%)	Hydrogen peroxide
[49]	1.5-fold	75	69	16 (23%)	Heat treatment and senescence

Maleck et al. [7] studied 10,000 EST clones obtained from the Arabidopsis Biological Resource Center representing approximately 7,000 genes. Schenk et al. [17] studied a custom array containing 2,375 ESTs with a biased representation of putative defense-associated and regulatory genes. From our estimate of redundancy (approximately 30%), this array contains 1,662 distinct genes. The study of Cheong et al. [48] involved the Affymetrix Arabidopsis Genome GeneChip array representing 8,200 genes. Desikan et al. [18] studied Arabidopsis Functional Genomics Consortium microarrays containing 11,000 EST clones representing approximately 7,800 distinct genes. The custom array of Swidzinski et al. [49] contained 75 ESTs previously implicated in programmed cell-death responses such as senescence and hypersensitive response.

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