Skip to main content

Table 3 The over- and under-amplified loci.

From: Statistical evaluation of transcriptomic data generated using the Affymetrix one-cycle, two-cycle and IVT-Express RNA labelling protocols with the Arabidopsis ATH1 microarray

Probe ID current 1-cyc vs. 2-cyc current IVT-E vs. 2-cyc Stepanova vs. Birnbaum AGI code Description
247762_at 16.4 39.8 2.4 AT5G59170 Proline-rich family protein.
249552_s_at 19.7 25.9 1.8 AT5G38250
AT5G38240
AT5G38250, serine/threonine protein kinase, putative; AT5G38240, serine/threonine protein kinase, putative.
251127_at 3.4 8.3 2.1 AT5G01080 Beta-galactosidase.
252971_at 10.9 22.5 1.6 AT4G38770 PRP4 (PROLINE-RICH PROTEIN 4).
255138_at 12.5 14.2 1.8 AT4G08380 Proline-rich extensin-like family protein.
262566_at 28.2 63.1 3.0 AT1G34310 ARF12 (AUXIN RESPONSE FACTOR 12); transcription factor.
266152_s_at 14.3 17.2 2.8 AT3G31908
AT3G32377
AT2G12050
AT3G31908, pseudogene, similar to aintegumenta-like protein; AT3G32377, pseudogene, similar to aintegumenta-like protein; AT2G12050, pseudogene, embryogenesis protein-related, similar to BABY BOOM (A. thaliana).
266154_at 39.1 47.1 3.0 AT2G12190 Cytochrome P450, putative.
245513_at 4.4 4.0 3.2 AT4G15780 ATVAMP724 (Arabidopsis thaliana vesicle-associated membrane protein 724).
245665_at 4.8 5.1 2.4 AT1G28250 Similar to hypothetical protein [Oryza sativa (japonica cultivar-group)] (GB:BAC84779.1).
246210_at 8.0 6.9 2.3 AT4G36420 Ribosomal protein L12 family protein.
249583_at 5.4 5.8 1.8 AT5G37770 TCH2 (TOUCH 2); calcium ion binding.
250226_at 7.4 6.6 3.6 AT5G13780 GCN5-related N-acetyltransferase, putative.
250935_at 9.0 8.9 39.7 AT5G03240 UBQ3 (POLYUBIQUITIN 3); protein binding.
253189_at 8.3 6.0 5.8 no_match No_match.
253464_at 6.8 4.7 3.4 AT4G32030 Unknown protein.
253545_at 5.4 7.4 4.0 AT4G31310 Avirulence-responsive protein-related/avirulence induced gene (AIG) protein-related.
256092_at 9.8 12.4 8.3 AT1G20696 HMGB3 (HIGH MOBILITY GROUP B 3); transcription factor.
256231_at 9.4 9.5 5.3 AT3G12630 Zinc finger (AN1-like) family protein.
258001_at 5.5 6.2 9.8 AT3G28950 Avirulence-responsive protein-related/avirulence induced gene (AIG) protein-related.
258397_at 6.1 6.1 1.9 AT3G15357 Unknown protein.
258958_at 7.0 10.4 4.6 AT3G01390 VMA10 (VACUOLAR MEMBRANE ATPASE 10).
259095_at 5.9 6.2 1.7 AT3G05020 ACP1 (ACYL CARRIER PROTEIN 1).
262295_at 7.7 4.9 4.4 AT1G27650 ATU2AF35A; RNA binding.
263878_s_at 4.7 4.4 3.8 AT3G18140
AT2G22040
AT3G18140, transducin family protein/WD-40 repeat family protein; AT2G22040, transducin family protein/WD-40 repeat family protein.
264566_at 6.8 4.6 5.6 AT1G05270 TraB family protein.
264702_at 5.3 5.3 3.0 AT1G70190 Ribosomal protein L12 family protein.
265103_at 12.9 4.2 3.9 AT1G31070 UDP-N-acetylglucosamine pyrophosphorylase-related.
265443_at 6.4 6.7 3.0 AT2G20750 ATEXPB1 (ARABIDOPSIS THALIANA EXPANSIN B1).
266074_at 5.1 8.1 1.7 AT2G18740 Small nuclear ribonucleoprotein E, putative/snRNP-E, putative/Sm protein E, putative.
266125_at 6.9 6.3 1.8 AT2G45050 Zinc finger (GATA type) family protein.
267064_at 6.8 7.9 2.9 AT2G41110 CAM2 (CALMODULIN-2); calcium ion binding.
AFFX-Athal-GAPDH_5_s_at 13.4 8.3 11.8 AT3G04120 GAPC (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE C SUBUNIT); glyceraldehyde-3-phosphate dehydrogenase.
  1. Loci classed as over- (above the break line) and under-amplified (below the break line) in both the data from this study and in independent one-cycle vs. two-cycle root data sets. Numbers represent the fold change in the comparison. Where several AGI codes are given for a particular probe ID, more than one transcript is likely to hybridise to the probes