Table 1.
Enrichment analysis of metabolic pathways grouped by k-means clustering.
Gene expression patterns were sorted into 16 clusters, as determined by k-means analysis of transcripts detected in the B73 maize inbred line after 0, 1, 4, 6 and 24 h of caterpillar feeding
| Cluster no. | No. of genes in the cluster | Description | No. of genes | FDR | |
|---|---|---|---|---|---|
| Group 1: strong increasing average (2 SD) | 1 | 133 | Benzoate biosynthesis II (CoA-independent, non-β-oxidative) | 3 | 3.3E−03 |
| Suberin biosynthesis | 3 | 6.9E−03 | |||
| Phenylpropanoid biosynthesis, initial reactions | 2 | 1.2E−02 | |||
| trans-Cinnamoyl-CoA biosynthesis | 2 | 1.2E−02 | |||
| Adenine and adenosine salvage VI | 2 | 1.2E−02 | |||
| 2 | 74 | S-Adenosyl-L-methionine cycle II | 4 | 1.4E−06 | |
| Jasmonic acid biosynthesis | 5 | 1.5E−06 | |||
| Methionine degradation I (to homocysteine) | 3 | 3.1E−05 | |||
| Traumatin and (Z)-3-hexen-1-yl acetate biosynthesis | 3 | 3.5E−05 | |||
| Divinyl ether biosynthesis II | 3 | 3.5E−05 | |||
| Linalool biosynthesis | 3 | 9.7E−05 | |||
| S-Adenosyl-L-methionine biosynthesis | 2 | 7.3E−04 | |||
| Ethylene biosynthesis from methionine | 3 | 9.8E−04 | |||
| 2′-Deoxymugineic acid phytosiderophore biosynthesis | 2 | 2.7E−03 | |||
| UDP-D-xylose and UDP-D-glucuronate biosynthesis | 2 | 4.1E−03 | |||
| Methylerythritol phosphate pathway | 2 | 4.1E−03 | |||
| Tryptophan biosynthesis | 2 | 6.5E−03 | |||
| Glycogen biosynthesis II (from UDP-D-glucose) | 2 | 7.8E−03 | |||
| Methionine biosynthesis II | 2 | 1.0E−02 | |||
| Colanic acid building blocks biosynthesis | 2 | 1.9E−02 | |||
| Galactose degradation III | 2 | 1.9E−02 | |||
| Group 2: moderately increasing average (approximately 1 SD) | 3 | 557 | Homogalacturonan biosynthesis | 5 | 1.0E−02 |
| Cellulose biosynthesis | 6 | 4.3E−02 | |||
| Cytokinins-O-glucoside biosynthesis | 8 | 4.3E−02 | |||
| 4 | 493 | Phenylpropanoid biosynthesis, initial reactions | 3 | 1.8E−02 | |
| trans-Cinnamoyl-CoA biosynthesis | 3 | 1.8E−02 | |||
| 5 | 357 | Sucrose degradation I | 4 | 1.7E−02 | |
| Suberin biosynthesis | 4 | 1.7E−02 | |||
| 6 | 207 | Jasmonic acid biosynthesis | 6 | 5.3E−05 | |
| Pyrimidine ribonucleosides degradation II | 3 | 5.7E−04 | |||
| Methylerythritol phosphate pathway | 3 | 1.1E−02 | |||
| β-Alanine biosynthesis II | 3 | 3.3E−02 | |||
| Glutamine biosynthesis III | 3 | 3.3E−02 | |||
| 7 | 562 | No results | |||
| 8 | 408 | Sucrose degradation III | 8 | 6.8E−04 | |
| Traumatin and (Z)-3-hexen-1-yl acetate biosynthesis | 3 | 1.7E−02 | |||
| Alanine degradation II (to D-lactate) | 3 | 1.7E−02 | |||
| Divinyl ether biosynthesis II | 3 | 1.7E−02 | |||
| Sucrose degradation I | 4 | 1.7E−02 | |||
| TCA cycle variation III (eukaryotic) | 5 | 1.7E−02 | |||
| CDP-diacylglycerol biosynthesis II | 4 | 1.8E−02 | |||
| CDP-diacylglycerol biosynthesis I | 4 | 1.8E−02 | |||
| Triacylglycerol biosynthesis | 4 | 2.5E−02 | |||
| Cyclopropane fatty acid biosynthesis | 3 | 2.9E−02 | |||
| Cyclopropane and cyclopropene fatty acid biosynthesis | 3 | 2.9E−02 | |||
| Glyoxylate cycle | 3 | 4.9E−02 | |||
| Pyrimidine ribonucleotides interconversion | 3 | 5.0E−02 | |||
| Group 3: moderately decreasing average (approximately 1 SD) | 9 | 456 | No results | ||
| 10 | 387 | Stachyose biosynthesis | 3 | 3.1E−02 | |
| 11 | 244 | Photorespiration | 5 | 4.4E−04 | |
| 12 | 399 | Luteolin biosynthesis | 3 | 1.3E−02 | |
| Leucodelphinidin biosynthesis | 4 | 1.3E−02 | |||
| Leucopelargonidin and leucocyanidin biosynthesis | 4 | 1.3E−02 | |||
| Flavonol biosynthesis | 3 | 3.2E−02 | |||
| Nitrogen fixation | 2 | 4.5E−02 | |||
| 13 | 500 | No results | |||
| 14 | 487 | No results | |||
| Group 4: moderately decreasing averages that significantly deviate from the population average (high FPKM) | 15 | 150 | Photosynthesis light reactions | 4 | 2.5E−05 |
| Calvin–Benson–Bassham cycle | 5 | 1.3E−03 | |||
| Gluconeogenesis I | 4 | 2.4E−02 | |||
| Glycine cleavage complex | 2 | 4.7E−02 | |||
| Glycolysis I | 4 | 4.7E−02 | |||
| 16 | 66 | Methylerythritol phosphate pathway | 2 | 5.2E−03 | |
| Cyanate degradation | 2 | 5.2E−03 | |||
| Photosynthesis light reactions | 2 | 5.2E−03 | |||
| Calvin–Benson–Bassham cycle | 3 | 5.2E−03 | |||
| Gluconeogenesis I | 3 | 7.2E−03 | |||
| Rubisco shunt | 2 | 3.8E−02 |