Skip to main content
. 2013 Jul 10;163(1):419–430. doi: 10.1104/pp.113.221481

Table I. Assignment of differentially expressed genes to the main functional categories (MapMan).

Functional categories containing more or fewer genes than expected (based on the distribution of functional categories of all genes represented on the microarray chip) are highlighted by + or −.

Bin Code Bin Namea All Genesb Wild Type versus rtcs t0 Directionc Pd Wild Type versus rtcs t2 Direction P Wild Type versus rtcs t4 Direction P
1 Photosynthesis 274 1 1
2 Major CHO metabolism 169 1 3 1
3 Minor CHO metabolism 171 1 1 4
4 Glycolysis 77
5 Fermentation 30 1 2 2
6 Gluconeogenesis/glyoxylate cycle 17
7 OPP 48
8 TCA/organic transformation 125 1 1
9 Mitochondrial electron-transport/ATP synthesis 157 1 1
10 Cell wall 552 7 12 + <0.01 19 + <0.01
11 Lipid metabolism 560 4 3 6
12 Nitrogen metabolism 50 1
13 Amino acid metabolism 383 2 1 2
14 Sulfur assimilation 15
15 Metal handling 73 1 2
16 Secondary metabolism 462 3 4 6
17 Hormone metabolism 586 5 5 12 0.23
18 Cofactor and vitamin metabolism 88
19 Tetrapyrrole synthesis 80 1
20 Stress 866 9 14 + 0.03 18 0.12
21 Redox regulation 251 1
22 Polyamine metabolism 24 1
23 Nucleotide metabolism 224 1
24 Biodegradation of xenobiotics 15 2 2
25 C1 metabolism 35 1 1
26 Miscellaneous 1,705 24 + <0.01 33 + <0.01 66 + <0.01
27 RNA 4,117 27 0.48 32 0.24 64 0.58
28 DNA 777 6 4 9
29 Protein 4,699 28 0.20 31 − 0.03 30 − <0.01
30 Signaling 1,542 7 11 0.34 14 0.07
31 Cell 1,025 7 8
32 MicroRNA, natural antisense 1 7
33 Development 657 5 11 0.05 19 + <0.01
34 Transport 1,340 10 0.99 17 0.21 19 0.90
35 Not assigned 16,256 128 0.40 156 0.76 237 0.99
Sume 37,451 279 353 546
a

Only the 35 main functional categories were considered.  bFunctional classification of all genes present on the microarray chip.  cFor direction, the column indicates if the functional category is overrepresented (+) or underrepresented (−) based on the comparison of detected and expected numbers of differentially expressed genes. The expected number is calculated based on the functional distribution of all genes on the microarray chip.  dP values are based on a χ2 test for independence with Yates’ continuity correction.  eAll genes that were assigned to a functional category by the MapMan software are summed up. This number is larger than the number of genes in the considered subset because numerous genes are assigned to more than one functional category. CHO, Carbohydrate; OPP, oxidative pentosephosphate pathway.