Table 1

A list of selected up-regulated genes and their functional categories
No Locus FC Gene ontology class Gene annotation detail
Response to stress and/or stress stimuli
1 At1g55920 2 response to cold AtSerat2;1_SAT1_SAT5__AtSerat2;1 (SERINE ACETYLTRANSFERASE 1)
2 At3g22840 1.94 response to cold ELIP1_ELIP__ELIP1 (EARLY LIGHT-INDUCABLE PROTEIN); chlorophyll binding
3 At1g10760 1.6 cold acclimation SEX1_GWD_SOP__SEX1 (STARCH EXCESS 1)
4 At1g09780 1.5 response to cold 2,3-biphosphoglycerate-independent phosphoglyceratemutase, putative/phosphoglyceromutase, putative
5 At4g26080 1.73 response to heat ABI1__ABI1 (ABA INSENSITIVE 1); calcium ion binding/protein serine/threonine phosphatase
6 At4g26850 1.61 response to heat VTC2__VTC2 (VITAMIN C DEFECTIVE 2)
7 At1g73330 3.09 response to water deprivation ATDR4__ATDR4 (Arabidopsis thaliana drought-repressed 4)
8 At3g11410 2.61 response to water deprivation AHG3_ATPP2CA__AHG3/ATPP2CA (ARABIDOPSIS THALIANA PROTEIN PHOSPHATASE 2CA); protein binding/protein serine/threonine phosphatase
9 At5g62470 2.25 response to salt stress AtMYB96_mybcov1_MYB96__MYB96 (myb domain protein 96); DNA binding/transcription factor
10 At3g61890 2.21 response to salt stress ATHB-12_ATHB12__ATHB-12 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 12); transcription factor
11 At2g46680 1.93 response to water deprivation ATHB-7_ATHB7__ATHB-7 (ARABIDOPSIS THALIANA HOMEOBOX 7)
12 At5g57050 1.87 response to osmotic stress ABI2__ABI2 (ABA INSENSITIVE 2)
13 At5g59780 1.84 response to salt stress AtMYB59_MYB59__MYB59 (myb domain protein 59); DNA binding/transcription factor
14 At5g37500 1.82 response to water deprivation GORK__GORK (GATED OUTWARDLY-RECTIFYING K+ CHANNEL); cyclic nucleotide binding/inward rectifier potassium channel/outward rectifier potassium channel
15 At4g34990 1.80 response to salt stress AtMYB32__AtMYB32 (myb domain protein 32); DNA binding/transcription factor
16 At1g29395 1.76 response to water deprivation COR414-TM1__COR414-TM1 (cold regulated 414 thylakoid membrane 1)
17 At1g02930 1.70 response to water deprivation ATGSTF6_ATGSTF3_ERD11_GST1_GSTF6__ATGSTF6 (EARLY RESPONSIVE TO DEHYDRATION 11); glutathione transferase
18 At3g19580 1.68 hyperosmotic salinity response AZF2__AZF2 (ARABIDOPSIS ZINC-FINGER PROTEIN 2)
19 At3g08720 1.67 response to salt stress ATS6K2_S6K2_ATPK19_ATPK2__ATPK19 (ARABIDOPSIS THALIANA PROTEIN KINASE 19); kinase
20 At2g30870 1.65 response to water deprivation ATGSTF10_ATGSTF4_ERD13__ATGSTF10 (EARLY DEHYDRATION-INDUCED 13); glutathione transferase
21 At4g30660 1.64 hyperosmotic salinity response hydrophobic protein, putative/low temperature and salt responsive protein, putative
22 At3g55730 1.61 response to salt stress AtMYB109_MYB109__MYB109 (myb domain protein 109); DNA binding/transcription factor
23 At3g03190 1.57 response to oxidative stress ATGSTF11_ATGSTF6__ATGSTF11 (GLUTATHIONE S-TRANSFERASE F11); glutathione transferase
24 At5g01600 1.74 response to hydrogen peroxide ATFER1__ATFER1 (FERRETIN 1); ferric iron binding
25 At2g16060 1.87 response to hypoxia AHB1_ARATH GLB1_ATGLB1_GLB1_NSHB1__AHB1 (ARABIDOPSIS HEMOGLOBIN 1)
26 At1g05200 1.56 response to light stimulus ATGLR3.4_GLR3.4_GLUR3__ATGLR3.4 (Arabidopsis thaliana glutamate receptor 3.4)
27 At5g64330 1.59 response to light stimulus NPH3_JK218_RPT3__NPH3 (NON-PHOTOTROPIC HYPOCOTYL 3)
28 At1g21590 1.63 response to stress protein kinase family protein
29 At2g35980 1.56 response to stress YLS9_NHL10__YLS9 (YELLOW-LEAF-SPECIFIC GENE 9)
30 At2g38470 2.0 defense response to fungus WRKY33__WRKY33 (WRKY DNA-binding protein 33); transcription factor
31 At1g12820 1.87 response to molecule of bacterial origin AFB3__AFB3 (AUXIN SIGNALING F-BOX 3); auxin binding/ubiquitin-protein ligase
32 At2g19190 1.80 defense response to bacterium FRK1__FRK1 (FLG22-INDUCED RECEPTOR-LIKE KINASE 1); kinase
33 At5g52450 1.73 response to nematode MATE efflux protein-related
34 At4g12480 1.65 defense response to fungus pEARLI 1__pEARLI 1; lipid binding
35 At1g24020 1.63 response to biotic stimulus MLP423__MLP423 (MLP-LIKE PROTEIN 423)
36 At2g24570 1.63 defense response to bacterium WRKY17__WRKY17 (WRKY DNA-binding protein 17); transcription factor
37 At5g64120 1.58 defense response to fungus peroxidase, putative
38 At5g58600 1.55 defense response to fungus PMR5__PMR5 (POWDERY MILDEW RESISTANT 5)
39 At3g11660 1.54 defense response to virus NHL1__NHL1 (NDR1/HIN1-like 1)
40 At5g50200 2.53 response to wounding ATNRT3.1_NRT3.1_WR3__WR3 (WOUND-RESPONSIVE 3); nitrate transmembrane transporter
41 At5g13930 1.51 response to wounding CHS_TT4__ATCHS/CHS/TT4 (CHALCONE SYNTHASE); naringenin-chalcone synthase
Sugar Accumulation
1 At1g56600 3.19 carbohydrate biosynthetic process ATGOLS2 (ARABIDOPSIS THALIANA GALACTINOL SYNTHASE 2); transferase, transferring glycosyl groups/transferase, transferring hexosyl groups
2 At5g18470 2.63 sugar binding curculin-like (mannose-binding) lectin family protein
3 At1g02460 2.46 carbohydrate metabolic process glycoside hydrolase family 28 protein/polygalacturonase (pectinase) family protein
4 At3g46970 1.85 carbohydrate metabolic process ATPHS2/PHS2 (ALPHA-GLUCAN PHOSPHORYLASE 2); phosphorylase/transferase, transferring glycosyl groups
5 At4g19810 1.84 carbohydrate metabolic process glycosyl hydrolase family 18 protein
6 At1g48100 1.84 carbohydrate metabolic process glycoside hydrolase family 28 protein/polygalacturonase (pectinase) family protein
7 At5g41670 1.79 pentose-phosphate shunt 6-phosphogluconate dehydrogenase family protein
8 At5g66460 1.75 carbohydrate metabolic process (1–4)-beta-mannanendohydrolase, putative
9 At3g18080 1.72 carbohydrate metabolic process glycosyl hydrolase family 1 protein
10 At2g44450 1.68 carbohydrate metabolic process glycosyl hydrolase family 1 protein
11 At4g27830 1.62 carbohydrate metabolic process glycosyl hydrolase family 1 protein
12 At4g09020 1.61 starch catabolic process; alpha-amylase activity ATISA3_ISA3__ATISA3/ISA3 (ISOAMYLASE 3); alpha-amylase
13 At3g61490 1.61 carbohydrate metabolic process glycoside hydrolase family 28 protein/polygalacturonase (pectinase) family protein
14 At1g10760 1.58 starch catabolic process SEX1_GWD_SOP__SEX1 (STARCH EXCESS 1)
15 At4g15210 1.54 starch catabolic process BMY1_ATBETA-AMY_AT-BETA-AMY_RAM1__ATBETA-AMY (BETA-AMYLASE); beta-amylase
16 At2g40840 1.5 starch catabolic process DPE2__DPE2 (DISPROPORTION ATING ENZYME 2); 4-alpha-glucanotransferase/heteroglycan binding
17 At1g03310 1.5 starch metabolic process ATISA2/BE2/DBE1/ISA2 (DEBRANCHING ENZYME 1); alpha-amylase/isoamylase
Lipid metabolism
1 At4g39670 4.88 glycolipid binding; molecular function unknown glycolipid binding/glycolipid transporter
2 At2g37870 2.25 lipid binding; lipid transport protease inhibitor/seed storage/lipid transfer protein (LTP) family protein
3 At2g24560 2.04 lipid metabolic process carboxylesterase
4 At3g22120 2.01 lipid transport; lipid binding CWLP (CELL WALL-PLASMA MEMBRANE LINKER PROTEIN); lipid binding
5 At5g55450 1.98 lipid transport; lipid binding protease inhibitor/seed storage/lipid transfer protein (LTP) family protein
6 At4g10955 1.75 lipid metabolic process lipase class 3 family protein
7 At4g12500 1.72 lipid binding protease inhibitor/seed storage/lipid transfer protein (LTP) family protein
8 At5g64080 1.71 lipid binding protease inhibitor/seed storage/lipid transfer protein (LTP) family protein
9 At2g38530 1.61 phospholipid transfer to membrane LTP2 (LIPID TRANSFER PROTEIN 2); lipid binding
ABA Responsive
1 At1g63840 3.27 Response to ABA stimulus; endome- mbrane system Zinc finger (C3HC4-type RING finger) family protein
2 At5g01540 3.22 response to abscisic acid stimulus lectin protein kinase, putative
3 At3g61890 2.21 response to abscisic acid stimulus ATHB-12 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 12); transcription factor
4 At1g69270 2.04 abscisic acid mediated signaling RPK1 (RECEPTOR-LIKE PROTEIN KINASE 1); kinase
Others
1 At1g21120 3.96 O-methyltransferase activity O-methyltransferase, putative
2 At1g78410 3.79 Response to oxidative stress; Molecular function unknown VQ motif-containing protein
3 At2g21210 3.31 Molecular function unknown auxin-responsive protein, putative
4 At5g06760 3.18 Molecular function unknown late embryogenesis abundant group 1 domain-containing protein/LEA group 1 domain-containing protein
5 At1g73330 3.09 response to water deprivation ATDR4__ATDR4 (Arabidopsis thaliana drought-repressed 4)
6 At1g24140 2.67 anchored to membrane matrixin family protein
7 At3g11410 2.61 response to water deprivation AHG3_ATPP2CA__AHG3/ATPP2CA (ARABIDOPSIS THALIANA PROTEIN PHOSPHATASE 2CA); protein binding/protein serine/threonine phosphatase
8 At2g15390 2.05 cell wall biogenesis; Fucosyltransferase activity FUT4 (fucosyltransferase 4); fucosyltransferase
9 At1g55920 1.97 response to cold AtSerat2;1_SAT1_SAT5__AtSerat2;1 (SERINE ACETYLTRANSFERASE 1)
10 At3g22840 1.94 response to cold ELIP1_ELIP__ELIP1 (EARLY LIGHT-INDUCABLE PROTEIN); chlorophyll binding
11 At3g55130 1.84 ATPase activity, coupled to transmembrane movement of substances ATWBC19 (WHITE-BROWN COMPLEX HOMOLOG 19); ATPase, coupled to transmembrane movement of substances
12 At4g26850 1.61 L-ascorbic acid biosynthetic process VTC2 (VITAMIN C DEFECTIVE 2)

Nair et al.

Nair et al. BMC Genomics 2012 13:643   doi:10.1186/1471-2164-13-643

Open Data