Table 1 Functional grouping of differentially expressed genes in aerial and root cells

 Amino acid metabolism

CAR1, GAD1, ARO9, ARO10

69 genes

 Purine, pyrimidine synthesis

24 genes

 Glycogen/trehalose

GLG2, GDB1, GPH1/TPS1, TPS2, TSL1, IGD1

 Nitrogen metabolism - other/Glycolysis, gluconeogenesis/Pentose phosphate shunt/ TCA, glyoxylate cycle/Carbohydrate metabolism - other/ Respiration, OxPhos/Cofactor, vitamins/Lipid metabolism

FBP26, ENO1, HXK1, PGK1, TDH1/GND2, NQM1, PRM15, SOL4, TKL2, YEF1 / IDP3, YPL113C/ALD2, ALD3, AMS1, FDH1, GAL7, GRE3, NCA2, SYM1, XKS1, XYL2, YDL124W, YIG1, YJR096W/COQ4, COA4, SHH4, RCF1, MCR1, NDE2/PCD1, THI4, THI11, YNL200C/AYR1, CTA1, ETR1, HES1, HMG2, HFD1, OPI10, SRT1, TGL1, FAA2, FOX2, POX2, POT1

DUR1,2, DAL1, DAL2, DAL3/FBP1, HXK2, PFK27/ TKL1, RKI1, SHB17/ACO2, CIT2, ICL1, MAE1, MLS1/ACS2, ACH1, ADH1, ADH3, ADH5, ADH6, ALD5, ALD6, DLD2, DLD3, GPI18, IMA5, MNN1, MTD1, PCS60/COQ2, CYC1, HEM1, HEM13, OYE2, Q0085, RCF2 YAH1/BUD16, BUD17, HEM3, ISU2, PAN6, PHO3, SPE4/CDS1, ERG3, ERG4, OLE1, SCS3, SUR2, SUR4

 Amino acids / purine, pyrimidine

AGP1, BAP2, BAP3, CAN1, DIP5, GAP1, HIP1, PUT4, SAM3, TAT1, TAT2, YMC1, YMC2 / FCY2, FCY22, FUI1, FUR4

 Nitrogen - other

ATO2, DAL4, DUR3, MEP1, MEP2, MEP3, TPO1

 Other transport: Sugars/Carbohydrates - other/Other ions/Others

GAL2, HXT5, HXT6, HXT14, YDL199C, YFL040W, VPS73/ − / CTR3, PMA2, MFM1, ADP1, PRM6/BPT1, PDR10, PDR18, PXA1, PXA2

HXT1, HXT2, HXT4, HXT13, HXT17/CRC1, CTP1, MPC2, JEN1, OAC1, ODC2, SFC1, VTC1, YAT1, YAT2, YHM2 / AST1, ENB1, FET3, FSF1, FTR1, GDT1, IZH4, MIR1, MMT1, PHO84, PHO88, PHO89, PMA1, PMP2, SIT1, ZRT1, ZRT2 / ANT1, AQR1, AQY2, ATR1, GDA1, GGC1, HNM1, OPT2, PET9, PRY2, PDR5, PTR2, RSB1, THI7, TNA1, VRG4

Meiosis, sporulation

134 genes

Cell wall (assembly, integrity)

DAN4, YGP1

CIS3, CRH1, FIT2, FKS1, GAS1, HSP150, KTR2, PUN1, SCW10, TOS1, TOS6, UTH1, UTR2, YPS3,

 Endocytosis, vesicle sorting/Mitochondria/Nucleus/Peroxisome

BTN2, COS4, EMP46, ERV29, GGA1, LSP1, ROD1, SIP3, SNX41, ERP3 / − / POM33/ PEX18, PEX22, PEX1

ART5, COS10, EMP70, MRS6, RTT10, YIP1/OXA1, PAM18/ BCP1, KAP123, NMD5, PSE1

 Autophagy/ Ubiquitin, proteasome/ Other

ATG2, ATG3, ATG7, ATG8, ATG9, ATG14, ATG16, ATG17, ATG34, ATG39, YOR152C/ GID COMPLEX: FYV10, VID22, VID28, VID30, RMD5; ASI1, CUZ1, ECM29, HUL4, RRI2, SAF1, UBC11, UBP2, UBR2, YUH1/ PAI3, PRD1, YBR139W

−/RFU1/−

General transcription

16 genes

General translation/tRNA production, Modification/Ribosome proteins/ Biogenesis

−/SOL1/−/RNP1, SRD1

27 genes/35 genes/127 genes/132 genes

 Transcription/Chromatin remodeling/ Translation, mRNA export, degradation/ Signaling

AZF1, CRF1 GCR1, MSA2, NRM1, XBP1 / ASF2, EPL1, ESC8, HST4, RIF1, RTT109, SPT21, SWI1/ HEF3, STO1, NGR1, MIP6 / AXL1, BEM4, BMH2, CYR1, FAR1, GIP2, HO, HYM1, KSP1, NNK1, PBP2, PHO92, PIG1, PIG2, PKH2, PRR2, RAD53, STE3, STE18, TEL1, TFS1, TPK1, TPK2, VHS3, VPS15

ARG80, CAF16, NRG1, SUT1, SUT2, VHR2 / FPR4, NPT1, SMP1, TOD6/ YIH1, ASC1, ANB1, DPH1, JJJ3, DPH2, ADF1, CAF20, CDC33, DPH5, DYS1, EFM1, EFM2, EFM4, GCD7, GCN3, LIA1, PUF6, RBG1, RRT2, SUP45, TEF1, TIF1, TIF5, TMA19/ PPT1, SPL2, INM1, YVH1

 Protein folding/Oxidative stress/Dessication/Other stress

ECM10, HSC82, HSP104, HSP26, HSP42, HSP78, HSP82, SSA1, SSA3, SSA4, SSE2, STI1, TMA17/CTT1, GPX1, GTO1, TRR2, RNY1/GRE1, SIP18, STF2/DCS2, DDR2, ECM4, GLO1, GTO3, HSP33, SED1, SNO4, SPG1, SPG4, YJL144W, YKL151C, YRO2/MSH2, PHR1, ULP2

EMC6, PAC10/ CCS1, FRM2, GPX2, SRX1, TRR1/−/−

Others

34 genes

6 genes

Unknown/dubious

158 genes

85 genes