Table 2. A list of the up-regulated transcripts belonging in different functional groups in P25
leaves
BIOTIC STRESS RELATED
Avr9/Cf-9 Elicitor or Hairpin elicited proteins
Chitinases, endochitinases
Disease resistance genes, putative
Enhanced disease susceptibility 1, EDS1
Hypersensitive cell death associated proteins
Miscellaneous
Pathogenesis related proteins, 1a, 1b, 1c, 4B, R, PX,
Receptor protein kinases
Retro element pol polyprotein
SAR-related proteins
TMV response-related gene product
Tumor-related protein precursors, putative
Total number of
positive
detections
138
21
17
21
2
10
7
30
3
5
19
1
2
CALCIUM BINDING, SIGNALLING AND
PHOSPHARYLATION RELATED
Ca-binding proteins
Calmodulins, calmodulin binding proteins
Kinase family proteins
Light signaling: PAR, Photo assimilate-responsive protein
MAP Kinase
Map kinase phosphatase
MAP kinases, MK1 and MAP3
Miscellaneous
Receptor kinases, various
Serine/threonine phosphatases
123
TRANSCRIPTION FACTORS AND SILENCING
RELATED
AGO2 (Argonaute 2), Putative
DCL2 (DICER-LIKE 2)
ERF-factors (ERF 1, 3 and 5)
LEAFY 1
Miscellaneous: transcription factors and RNA processing
NAC and Nam-domains containing proteins
RNA-directed RNA polymerase 1
SCARECROW gene regulator
Transcriptional activator PTI5; Pathogenesis-related
WRKY domain transcription factor family
87
SECONDARY METABOLITE RELATED
5-epi-aristolochene synthase
18
17
30
5
2
1
7
9
32
2
Range of fold change
enhancement
2-12 x
50 - 147 x
2 - 42 x
4-8x
2 - 18 x
3 - 38 x
5 - 3061 x
2x
2 - 10 x
10 - 280 x
9x
9x
2 - 26 x
2 - 25 x
3 - 14 x
8 - 424 x
2-3x
6x
2-8x
6 - 13 x
2 - 26 x
4x
1
1
5
4x
8x
5 - 12 x
33
13
1
2
2
29
2 - 10 x
2 - 41 x
4x
2-3 x
18 - 41 x
2 - 58 x
50
18
7 – 199 x
REF/SRPP-like protein, isoprenoids
Various secondary metabolite biosynthesis related
3
30
PROTEIN SYNTHESIS, TARGETING,
MODIFICATION AND DEGRADATION RELATED
Hydrolases, various
Nitrilases
Proteases, endopeptidases and carboxypeptidases
Protein disulfide isomerases
Protein kinases, various
Protein phosphatases, various
Protein secretion: ER lumen, vesicles, peroxisomes,
nucleus
Proteinase inhibitors
Transcription initiation (sigma factors)
Translation machinery and initiation - related proteins
Ubiquitination related, various
148
DEVELOPMENTAL, CELL CYCLE AND
CYTOSCELETON RELATED
Actin
Actin depolymerizing factors
DYNAMIN-LIKE 1E, putative
Embryo-abundant protein, putative
RabGAP/TBC/microtubule-associated protein
Senescence-associated proteins
Spindle disassembly related protein CDC48
Storage proteins (patatin, cupin)
WD-repeat protein /TTG1 (TRANSPARENT TESTA
GLABRA 1)
Yippee-like protein related cluster
22
4-5x
2- 18 x
11
2
28
2
25
5
19
2 - 162 x
2x
2 - 181 x
8x
2-5x
2-9x
2 - 33 x
4
3
9
40
3 - 99 x
25 – 58.8x
2 - 33 x
2 - 70 x
1
2
1
7
1
3
1
3
1
5x
2x
6x
4-5x
2x
2-3x
2x
4 - 10 x
2x
2
48 - 107 x
HORMONE METABOLISM RELATED
Auxin responsive proteins
Auxin independent proteins
Ethylene synthesis
Ethylene induced / responsive elements
Gibberellin related: receptors, oxidases
Lipoxygenases
Multiprotein bridging factor 1, putative
37
6
2
7
4
5
8
5
2-7x
2x
3 - 95 x
6 - 40 x
4-9x
3-8x
2 - 31 x
LIPID METABOLISM AND MEMBRANE
ASSOCIATED
Enoyl-CoA hydratase / Fatty oxidation complex
Lipid transfer protein 1 (e.g. LTP1)
Membrane & lipid modification activities
Membrane proteins, various
Phospholipases
41
7
6
9
15
4
2-4x
2 - 94 x
2 - 11 x
2 - 12 x
2-7x
GLUTATHIONE S-TRANSFERASES
Glutathione S-transferase
MAPEG (Membrane Associated, Eicosanoid and
Glutathione metabolism)
44
42
2
2 - 80 x
2-3x
ABIOTIC STRESS
Development and cell death domain + B protein
Heat shock protein 17.9
Oxidative stress response
Salt, drought, cold stress responsive proteins
41
3
26
4
8
4-6x
2-7x
11 x
2 - 73 x
NUCLEOTIDE BINDING AND PROCESSING
PROTEINS
AAA ATPase
ATP binding protein, putative
GTP binding protein RAP, RAS, Small G-proteins
Nucleotide processing
CELL WALL RELATED
Acetylglucosaminyltransferase, putative
Cell wall proteins
Glucan endo-1,3-beta-glucosidase
Hydroxy proline-rich glycoprotein
Pectin methylesterase inhibitor family protein, putative
S-adenosylmethionine decarboxylase
Xyloglucan endotransglucosylase-hydrolase
31
CYTOCHROME P450
Cytochrome p450 related
21
21
2 - 63 x
SUGAR AND AMINO ACID METABOLISM
Reductases, oxidoreductases, thioredoxins, various
Glycosyltransferases, various
Dehydrogenases, various
Decarboxylases, kinases
Aconitases, epimerases, invertases, amylases,
fructosidases, mutases, hydrolases, isomerases
Peroxidases
Oxidases
Mitochondrial electron transfer
Amino-, acyl- , acetyltransferases, Thiolases
Miscellaneous
138
29
20
27
8
21
2 - 39 x
2 - 30 x
2 - 24 x
2 - 10 x
2 - 23 x
17
4
5
11
6
2 - 14 x
12 - 2 x
2-7x
2 - 17 x
3-2x
TRANSPORT RELATED
Amino acid and Oligopeptide transporter proteins
Ion channels
81
17
8
2 - 25 x
3 - 26 x
12
6
8
5
26
2
6
6
2
2
1
9
3 - 70 x
2-9x
2-3x
2-4x
3x
3 - 20 x
8 - 66 x
2-7x
2 - 20 x
3x
3 - 14 x
Multidrug resistance proteins /ABC transporters
Phosphate, sulphate, ammonium, metal, nitrate transport
Sugar transporters
Transport related, miscellaneous
13
21
7
15
DNA-BINDING PROTEINS
DNA binding protein, putative
Drm3-like protein
Ku70-like protein
Microsatellite DNA
Sister chromatid cohesion 1 protein, low query coverage
11
4
1
1
4
1
FUNCTIONS NOT ASSIGNED
miscellaneous
39
39
UNIDENTIFIED
DUF domains
others
269
12
257
3-8x
2 - 17 x
2-7x
2 - 17 x
2-9x
2x
3-4x
2 - 44 x
2 - 120 x
The table represents the total number of detections of transcripts that were up-regulated more than twofold in the P25-expressing plants. Statistical significance was tested by using student t-test (p<0.05) with
the BH false discovery rate of 5%.