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Table 1 Genes with anti-directional regulation by low and high media pH. High pH data derived from the present study, low pH data are taken from Lager et al. [14]

From: pH-dependent transcriptional profile changes in iron-deficient Arabidopsis roots

Locus Description High pH Low pH (1 h) Low pH (8 h) High/low pH ratio
Foldchange
AT2G41810 Imidazolonepropionase 13.56   0.06 214.45
AT4G01630 EXP17, expansin A17 4.32 0.10   43.85
AT1G43800 SAD6, plant stearoyl-acyl-carrier-protein desaturase family protein 4.26   0.10 42.98
AT1G09750 Eukaryotic aspartyl protease family protein 2.68   0.07 39.09
AT1G33840 Protein of unknown function (DUF567) 10.88 0.28   38.25
AT4G26050 PIRL8, plant intracellular ras group-related LRR 8 8.22 0.23   35.38
AT1G50050 CAP (Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis-related 1 protein) superfamily protein 5.69   0.20 28.49
AT2G43890 Pectin lyase-like superfamily protein 6.32   0.23 26.91
AT5G48430 Eukaryotic aspartyl protease family protein 6.61 0.30   21.76
AT4G33560 WIP5, wound-responsive family protein 4.06   0.27 15.26
AT2G43620 Chitinase family protein 6.43   0.44 14.52
AT1G16510 SAUR41, SAUR-like auxin-responsive protein family 3.94 0.28   14.13
AT5G45340 CYP707A3, cytochrome P450, family 707, subfamily A, polypeptide 3 3.15 0.23   13.62
AT5G60770 NRT2.4, nitrate transporter 2.4 5.60   0.42 13.30
AT3G47380 ATPMEI11, plant invertase/pectin methylesterase inhibitor superfamily protein 4.07   0.31 13.00
AT3G12830 SAUR72, SAUR-like auxin-responsive protein family 3.05 0.33   9.33
AT4G10270 WIP4, WOUND-RESPONSIVE FAMILY PROTEIN 3.41 0.46   7.37
AT5G39890 PCO2, PLANT CYSTEINE OXIDASE 2 2.88   0.43 6.78
AT5G15230 GASA4, GAST1 protein homolog 4 2.98 0.45   6.58
AT1G05300 ZIP5, zinc transporter 5 precursor 3.11 0.50   6.25
AT3G10040 HRA1, HYPOXIA RESPONSE ATTENUATOR1 3.07   0.49 6.19
AT3G27220 Galactose oxidase/kelch repeat superfamily protein 2.77   0.45 6.11
AT5G66460 MAN7, glycosyl hydrolase superfamily protein 2.18   0.43 5.07
AT4G02290 GH9B13, glycosyl hydrolase 9B13 2.35   0.47 4.99
AT1G67750 Pectate lyase family protein 2.31 0.47   4.89
AT1G70710 CEL1, GH9B1, glycosyl hydrolase 9B1 2.24 0.49   4.57
AT4G19230 CYP707A1, cytochrome P450, family 707, subfamily A, polypeptide 1 2.14   0.48 4.44
AT2G29330 TRI, TROPINONE REDUCTASE 0.49   2.28 0.22
AT1G35260 MLP165, MLP-LIKE PROTEIN 165 0.47   2.26 0.21
AT4G38470 Dehydrin family protein 0.47   2.31 0.20
AT5G13750 ZIFL1, ZINC INDUCED FACILITATOR-LIKE 1 0.38   2.05 0.18
AT4G15610 Uncharacterized protein family 0.45   2.45 0.18
AT3G21690 MATE efflux family protein 0.41   2.31 0.18
AT5G66170 STR18, SULFURTRANSFERASE 18 0.41   2.41 0.17
AT1G13600 BZIP58, BASIC LEUCINE-ZIPPER 58 0.45 2.65   0.17
AT3G14990 DJ1A, DJ-1 HOMOLOG A 0.41   2.42 0.17
AT1G65310 XTH17, XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 17     
  0.49 2.95   0.17  
AT2G32150 Haloacid dehalogenase-like hydrolase (HAD) superfamily protein 0.49   3.13 0.16
AT1G55920 SAT1, SERINE ACETYLTRANSFERASE 1 0.36 2.56   0.14
AT2G39380 EXO70H2, EXOCYST SUBUNIT EXO70 FAMILY PROTEIN H2 0.39   2.78 0.14
AT4G38540 FAD/NAD(P)-binding oxidoreductase family protein 0.40   2.88 0.14
AT3G11340 UGT76B1, UDP-DEPENDENT GLYCOSYLTRANSFERASE 76B1 0.34   2.47 0.14
AT1G53990 GLIP3, GDSL-MOTIF LIPASE 3 0.31   2.27 0.14
AT1G67810 SUFE2, SULFUR E2 0.32 2.35   0.13
AT1G55850 CSLE1, CELLULOSE SYNTHASE LIKE E1 0.42   3.37 0.12
AT5G37260 CIR1, CIRCADIAN 1 0.32 2.63   0.12
AT3G22370 AOX1A, ALTERNATIVE OXIDASE 1A 0.34   2.85 0.12
AT1G01720 ANAC2, ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 2 0.46 4.12   0.11
AT4G30670 Putative membrane lipoprotein 0.28   2.65 0.10
AT1G43160 RAP2.6, RELATED TO AP2 6 0.33   3.21 0.10
AT2G29490 GSTU1, GLUTATHIONE S-TRANSFERASE TAU 1 0.24   2.32 0.10
AT1G51420 SPP1, SUCROSE-PHOSPHATASE 1 0.41   4.06 0.10
AT1G49570 Peroxidase superfamily protein 0.43   4.36 0.10
AT1G77450 ANAC032, NAC DOMAIN CONTAINING PROTEIN 32 0.27 2.91   0.09
AT1G73260 KTI1, KUNITZ TRYPSIN INHIBITOR 1 0.33   3.75 0.09
AT1G80240 DGR1, DUF642 L-GALL RESPONSIVE GENE 1 0.25 2.95   0.08
AT3G46230 HSP17.4, HEAT SHOCK PROTEIN 17.4, 0.17   2.03 0.08
AT1G17180 GSTU25, GLUTATHIONE S-TRANSFERASE TAU 25 0.17 2.18   0.08
AT5G24090 CHIA, CHITINASE A 0.29   3.94 0.07
AT3G01420 DOX1, PLANT ALPHA DIOXYGENASE 1 0.25   3.53 0.07
AT5G25460 DGR2, DUF642 L-GALL RESPONSIVE GENE 2 0.38   5.47 0.07
AT4G13180 NAD(P)-binding Rossmann-fold superfamily protein 0.20 3.16   0.06
AT2G29420 ATGSTU7, GLUTATHIONE S-TRANSFERASE TAU 7 0.22   3.64 0.06
AT5G61820 Stress up-regulated Nod 19 protein 0.17   2.96 0.06
AT2G22860 PSK2, PHYTOSULFOKINE 2 PRECURSOR 0.23   4.08 0.06
AT1G76520 PILS3, PIN-LIKES 3 0.14 2.66   0.05
AT5G50760 SAUR55, SMALL AUXIN UPREGULATED RNA 55 0.32   6.13 0.05
AT1G05340 ATHCYSTM1, CYSTEINE-RICH TRANSMEMBRANE MODULE 1 0.40   8.31 0.05
AT2G46750 GULLO2, L -GULONO-1,4-LACTONE (L -GULL) OXIDASE 2 0.20   4.62 0.04
AT1G78340 GSTU22, GLUTATHIONE S-TRANSFERASE TAU 22 0.12 2.72   0.04
AT5G49450 BZIP1, BASIC LEUCINE-ZIPPER 1 0.22   6.01 0.04
AT5G47990 CYP705A5, CYTOCHROME P450, FAMILY 705, SUBFAMILY A, POLYPEPTIDE 5 0.07   2.05 0.04
AT1G02850 BGLU11, BETA GLUCOSIDASE 11 0.30   9.09 0.03
AT2G17500 PILS5, PIN-LIKES 5 0.08   2.45 0.03
AT5G13080 WRKY, WRKY DNA-BINDING PROTEIN 75 0.20   6.49 0.03
AT2G41380 S-adenosyl-L-methionine-dependent methyltransferases superfamily protein 0.06 2.09   0.03
AT3G09270 GSTU8, GLUTATHIONE S-TRANSFERASE TAU 8 0.13   5.50 0.02
AT1G61560 MLO6, MILDEW RESISTANCE LOCUS O 6 0.18   7.34 0.02
AT1G21100 IGMT1, INDOLE GLUCOSINOLATE O-METHYLTRANSFERASE 1 0.09   3.96 0.02
AT4G22610 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein 0.11   5.37 0.02
AT5G48010 ATTHAS1, THALIANOL SYNTHASE, THALIANOL SYNTHASE 1 0.05   3.00 0.02
AT2G15490 UGT73B4, UDP-GLYCOSYLTRANSFERASE 73B4 0.05 3.06   0.02
AT5G06860 PGIP1, POLYGALACTURONASE INHIBITING PROTEIN 1 0.06 4.10   0.01
AT3G13950 Ankyrin 0.06   7.14 0.01
AT1G17170 ATGSTU24, GLUTATHIONE S-TRANSFERASE TAU 24 0.13   18.19 0.01
AT5G22890 STOP2, SENSITIVE TO PROTON RHIZOTOXICITY 2 0.01 2.09   0.01
AT1G05680 UGT74E2, uridine diphosphate glycosyltransferase 74E2 0.01   3.45 0.00
AT1G51840 SIF1, STRESS INDUCED FACTOR 1 0.03   10.81 0.00
AT1G08430 ALMT1, ALUMINUM-ACTIVATED MALATE TRANSPORTER 1 0.03   15.97 0.00
AT1G51830 SIF1, STRESS INDUCED FACTOR 1 0.02   9.67 0.00
AT4G31940 CYP82C4, CYTOCHROME P450, FAMILY 82, SUBFAMILY C, POLYPEPTIDE 4 0.00 2.90   0.00