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. 2005 Nov;139(3):1518–1528. doi: 10.1104/pp.105.068684

Table I.

Transcriptome differences between CpNifS overexpressors and wild-type plants

Wild-type (ecotype Ws) and CpNifS-overexpressing (NifS55 and NifS38) Arabidopsis plants were grown on control medium (MS) or with 40 μm selenate (Se) for 10 d, and transcriptomes of root RNA were analyzed using Affymetrix GeneChip arrays as described in “Materials and Methods.” Two sets of experiments (set 1 and set 2) were carried out separately to evaluate the reproducibility of the results. Genes showing more than 2-fold differences between the wild type and CpNifS overexpressors either on MS or Se conditions were selected by comparing the normalized signals and calculating their ratios, as shown in the NifS55/Ws and Nif38/Ws columns. The significance of the difference is represented by superscript letters, which describe the up and down effects of NifS overexpression on gene expression by fold change differences: a, >5.00; b, >2.00; c, >1.33; d, <0.75; e, <0.50. Regulation by Se (Se/MS ratio) is indicated using the same superscript letters. The absolute calls of each transcript (P, present; M, marginal; A, absent) are indicated on the right-hand side of the normalized values. The relative ratios are calculated for the pairs having “present” call at least in one sample.

Affy Code
AGI Locus
Annotation
Set 1
Set 2
Ws
NifS55
NifS55/Ws
Ws
NifS38
NifS38/Ws
Se MS Se/MS Se MS Se/MS Se MS Se MS Se/MS Se MS Se/MS Se MS
261744_at AT1G08490 NifS 1.16 P 1.03 P 1.12 41.32 P 47.44 P 0.87 35.71a 46.10a 0.89 P 0.75 P 1.19 24.52 P 20.01 P 1.23 27.46a 26.75a
259161_at AT3G01500 Carbonic anhydrase 1 0.33 A 9.36 P 0.04e 2.03 A 0.42 A 0.04e 0.25 A 8.47 P 0.03e 0.73 A 3.30 A 0.39e
258897_at AT3G05730 Expressed protein 0.39 A 1.08 P 0.36e 1.33 P 0.41 P 3.22b 3.41b 0.38e 0.49 A 1.07 P 0.46e 1.16 P 1.75 P 0.66d 2.36b 1.64c
252537_at AT3G45710 Proton-dependent oligopeptide transporter family 0.25 P 1.16 P 0.22e 0.84 P 1.49 P 0.56d 3.35b 1.29 0.17 P 0.82 P 0.21e 0.45 P 0.66 P 0.68d 2.57b 0.81
260535_at AT2G43390 Expressed protein 0.61 P 1.13 P 0.54d 1.56 P 1.44 P 1.09 2.55 1.28 0.71 A 1.42 P 0.50d 1.50 P 1.75 P 0.86 2.10b 1.23
251974_at AT3G53200 Myb family transcription factor (MYB27) 0.64 M 1.33 P 0.48e 1.46 P 2.67 P 0.55d 2.27 2.00b 0.84 P 1.13 P 0.74d 1.78 P 1.62 P 1.10 2.11b 1.43c
264263_at AT1G09155 SKP1 interacting partner 3-related 0.51 A 0.69 P 0.74d 1.10 P 1.66 P 0.66d 2.15 2.39b 0.46 A 1.58 P 0.29e 1.19 P 0.90 P 1.33 2.59b 0.57d
255054_s_at AT4G23560 Glycosyl hydrolase family 9 protein similar to cellulase 1.44 P 0.80 P 1.80c 0.73 P 2.41 P 0.30e 0.51d 3.02b 0.45 A 0.82 M 0.99 P 1.73 P 0.57d 2.21b 2.11b
246340_s_at AT3G44860 S-Adenosylmethionine:carboxyl methyltransferase family 15.18 P 0.65 A 23.50a 5.93 P 1.33 P 4.45b 0.39e 2.06b 10.71 P 0.35 A 30.34a 7.94 P 1.18 P 6.75a 0.74d 3.33b
247905_at AT5G57400 Hypothetical protein 0.73 P 1.00 A 0.72d 0.87 P 2.02 P 0.43e 1.20 2.01b 1.07 A 0.76 M 1.15 A 1.70 P 0.68d 2.23b
265400_at AT2G10940 Protease inhibitor/seed storage/LTP family 0.30 A 2.86 P 0.10e 0.33 A 0.77 A 0.27e 0.64 A 3.56 P 0.18e 0.91 A 1.63 A 0.46e
249390_at AT5G39740 60S ribosomal protein L5 1.35 A 1.09 P 1.23 1.09 A 0.30 A 3.66b 0.27e 0.86 A 1.36 P 0.63d 1.04 A 0.29 A 0.21e
263369_at AT2G20480 Expressed protein 1.38 P 1.32 P 1.05 1.05 P 0.45 A 2.32b 0.76 0.34e 0.89 P 1.07 P 0.83 0.44 A 0.40 A 0.49e 0.37e
261197_at AT1G12900 Glyceraldehyde 3-phosphate dehydrogenase, putative 0.99 P 2.06 P 0.48e 0.69 A 0.53 A 0.70d 0.26e 0.88 A 2.36 P 0.37e 0.89 A 1.13 A 0.48e
256825_at AT3G22120 Protease inhibitor/seed storage/LTP family 1.01 P 1.11 P 0.91 0.66 P 0.51 P 1.30 0.65d 0.46e 1.25 M 1.12 P 1.12 0.83 A 0.10 A 8.17a 0.09e
262586_at AT1G15480 DNA-binding protein, putative 1.32 P 1.09 P 1.21 0.61 P 0.14 A 4.42b 0.46e 0.13e 1.59 P 1.35 P 1.18 0.33 P 0.51 A 0.64d 0.21e 0.38e
253060_at AT4G37710 VQ motif-containing protein 8.73 P 0.90 A 9.68a 4.01 A 0.63 A 0.46e 9.59 P 0.49 A 19.74a 4.75 P 0.38 A 12.57a 0.50e
264718_at AT1G70130 Lectin protein kinase, putative 4.86 P 0.45 A 10.93a 1.08 A 0.44 A 0.22e 6.94 P 1.23 A 5.64a 2.99 A 0.92 A 0.43e