Table 3.
trans-Prenyltransferase genes and isoprenoid pathway gene co-expressions in A. thaliana.
| CYTOSOL AND MITOCHONDRIA | ||||||||||
| Pathway | MVA | Sterol | Triterpenoids | Sesquiterpenoids/Diterpenoids | Protein Prenylation | Ubiquinone | ||||
| Total No. of Genes per Pathway | 9 | 24 | 13 | 13 | 7 | 4 | ||||
| FPPS1 | At5g47770 | 6 | 13 | 2 | 1 | 4 | 0 | |||
| FPPS2 | At4g17190 | 7 | 14 | 0 | 1 | 3 | 1 | |||
| GGPPS1 | At1g49530 | 0 | 0 | 2 | 0 | 0 | 3 | |||
| GGPPS3 | At2g18640 | 0 | 4 | 3 | 6 | 1 | 2 | |||
| GGPPS11 | At4g36810 | 0 | 11 | 2 | 0 | 1 | 0 | |||
| GGPPS4 | At2g23800 | 2 | 2 | 3 | 1 | 0 | 2 | |||
| PPPS1 | At2g34630 | 2 | 3 | 0 | 2 | 1 | 4 | |||
| PLASTIDS | ||||||||||
| Pathway | MEP | Plastoquinone | Chlorophyll | Carotenoid | Phylloquinone | Gibberellins | Monoterpenoids | Diterpenoids/Sesquiterpenoids | Sesterterpenoids | |
| Total No. of Genes per Pathway | 7 | 6 | 37 | 32 | 7 | 23 | 6 | 13 | 3 | |
| SSU | At4g38460 | 5 | 5 | 25 | 22 | 0 | 5 | 2 | 1 | 0 |
| GGPPS11 | At4g36810 | 7 | 3 | 29 | 18 | 1 | 7 | 1 | 0 | 0 |
| GGPPS2 | At2g18620 | 0 | 0 | 3 | 1 | 5 | 2 | 2 | 7 | 1 |
| GFPPS1 | At3g14530 | 0 | 0 | 1 | 0 | 3 | 2 | 0 | 5 | 2 |
| GGPPS3 | At3g29430 | 0 | 0 | 4 | 0 | 4 | 2 | 2 | 8 | 1 |
| GGPPS4 | At3g32040 | 0 | 0 | 3 | 0 | 5 | 7 | 2 | 7 | 1 |
| PPPS2 | At3g20160 | 0 | 0 | 4 | 0 | 4 | 4 | 2 | 8 | 1 |
| PPPS1 | At2g34630 | 0 | 0 | 0 | 2 | 4 | 2 | 4 | 2 | 1 |
| SPPS1 | At1g78510 | 6 | 6 | 29 | 20 | 0 | 4 | 2 | 1 | 0 |
| SPPS2 | At1g17050 | 7 | 4 | 29 | 22 | 0 | 7 | 2 | 1 | 0 |
Table 3 shows number of pathway genes that are significantly co-expressed with the trans-PTs. The intensity of the highlighted background is directly proportional to the relative number of co-expressed genes/total number of pathway genes. Data for co-expression analysis were obtained from BAR/Expression Browser (http://bar.utoronto.ca/affydb/cgi-bin/affy_db_exprss_browser_in.cgi) and log2 transformed (see Table S2 for log2 transformed expression data). In general, AtGeneExpress_plus-Extended Tissue Series data/Average of replicate treatments were downloaded. Genes that are missing were not present on the microarrays, and therefore, they are not included in the analysis. Pearson correlation coefficients and the corresponding false discovery rate (FDR) p-values were calculated. The threshold for significance is p-value ≤ 0.05. A detailed description of the analysis can be found in [54]. Genes in categories mono-, di-, sesqui-, sester- and triterpenoids contain genes encoding only terpene cyclases. Genes in the category diterpenoids/sesquiterpenoids and sesquiterpenoids/diterpenoids partly overlap. In both categories were kept the genes that have no experimentally proven one or other activity, and plastidial genes were considered diterpenoids and kept only in the category diterpenoids/sesquiterpenoids.