Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip®Soybean Genome Array: optimizing analysis by masking biased probes

Table 1 Purine-ureide pathway genes used for qRT-PCR validation.

		ANOVA¹		Log₂(N/L)²
Annotation	Probe Set ID	No mask	Mask	No mask	Mask	ΔΔC_T
GAR Synthetase [GARS (pur2)]	Gma.8431.1.S1_at	-	+	0.9	1.8	5.5
GAR transformylase [GART (pur3)]	Gma.16.1.S1_s_at	+	+	2.6	3.8	4.5
FGAR amidotransferase [FGARAT (pur4)]	Gma.12152.1.S1_at	+	+	3.8	4.1	5.3
AIR synthase [AIRS (pur5)]	Gma.5959.1.S1_at	-	+	1.3	4.7	4.1
AIR carboxylase [AIRC (pur6)]	Gma.7887.1.S1_at	+	+	1.8	3.3	3.1
SAICAR synthetase [SAICARS (pur7)]	Gma.4693.1.S1_at	-	+	0.1	5.2	5.4
SAICAR lyase [ASAL (pur8)]	GmaAffx.86903.1.S1_at	+	+	3.4	3.6	2.6
AICAR transformylase/IMP synthase [AICART (pur9/10)]	GmaAffx.89959.1.S1_at	+	+	2.8	3.8	4.0
IMP dehydrogenase [IMPDH]	Gma.1685.1.S1_at	-	+	1.4	6.3	7.1
Adenine phosphorybosyltransferase [APRT]	Gma.5292.1.S1_a_at	+	+	3.6	4.3	3.5
Adenylate kinase [ADK]	GmaAffx.92905.1.S1_s_at	+	+	2.8	3.4	3.1
Uricase [Uricase]	GmaAffx.93267.1.S1_s_at	+	+	3.0	4.1	6.8
Allantoinase [Allantoinase]	GmaAffx.87486.1.S1_at	-	+	1.2	2.2	1.2

¹ + indicates genes that were detected as differentially-expressed among three different organs after an ANOVA (p < 0.0001, FDR < 0.0015, ≥ 2-fold difference) using the common bean CSH GeneChip data with no masking or after masking with a signal intensity threshold of 80.
² Log₂ (nodule/leaf) value obtained from the common bean CSH GeneChip data with no masking or after masking with a signal intensity threshold of 80.
³ ΔΔC_T = [C_T(leaf) - C_T(18s)] - [C_T(nodule) - C_T(18s)] from qRT-PCR data. C_T18s rRNA values were stable in the organs examined and were used to normalize the data.

ISSN: 1471-2229