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1.
Figure 6

Figure 6. From: Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling.

Summary of the set of protein-protein interactions revealed by the two-hybrid assays. Interactions were compiled and displayed using the Cytoscape software package.

Arthur G Hunt, et al. BMC Genomics. 2008;9:220-220.
2.
Figure 2

Figure 2. From: Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling.

Normalized expression of Arabidopsis polyadenylation-related genes in mature pollen. The values for each gene in the array analysis of mature pollen were plotted as shown.

Arthur G Hunt, et al. BMC Genomics. 2008;9:220-220.
3.
Figure 8

Figure 8. From: Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling.

Summary of the set of protein-protein interactions involving proteins whose genes are expressed in pollen. Proteins whose genes are not expressed in pollen (see Figure 2) were removed from the network shown in Figure 6 and the results displayed using Cytoscape.

Arthur G Hunt, et al. BMC Genomics. 2008;9:220-220.
4.
Figure 7

Figure 7. From: Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling.

Summary of the set of protein-protein interactions involving the products of constitutively-expressed genes. Proteins corresponding to those genes that are expressed only in specialized tissues or times of development (PAPS3, PCFS1, and PCFS5) were removed from the network shown in Figure 6.

Arthur G Hunt, et al. BMC Genomics. 2008;9:220-220.
5.
Figure 4

Figure 4. From: Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling.

Meta-analysis of Arabidopsis poly(A) factor gene expression in response to chemicals and hormones. Normalized expression data for the NASC Arabidopsis chemical/hormone series (Additional file 1) were extracted and plotted as shown. The legends indicate the correspondence between the plots and the respective Arabidopsis gene identification designation. The numerical key for each array experiment is given along the X-axis, and the detail can be found in Additional file 1. The single arrows indicate the position for cycloheximide; double arrows for GA mutants; empty arrows for imbibition and ABA treatment.

Arthur G Hunt, et al. BMC Genomics. 2008;9:220-220.
6.
Figure 5

Figure 5. From: Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling.

Meta-analysis of Arabidopsis poly(A) factor gene expression in response to biotic stress and different light treatments. Normalized expression data for the NASC Arabidopsis biotic stress series (Additional file 1) were extracted and plotted as shown. The legends indicate the correspondence between the plots and the respective Arabidopsis gene identification designation. The numerical key for each array experiment is given along the X-axis. While the full list of the agents can be found in Additional file 1, here is a brief list: 1–16, control and Pseudomonas syringae infection; 17–22, control and Phytophthora infection; 23–36, control and elicitors treatment; 37–52, dark and different light treatment.

Arthur G Hunt, et al. BMC Genomics. 2008;9:220-220.
7.
Figure 3

Figure 3. From: Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling.

Meta-analysis of Arabidopsis poly(A) factor gene expression in different abiotic stress conditions. Normalized expression data for the NASC Arabidopsis abiotic stress series (Additional file 1) were extracted and plotted as shown. The legends indicate the correspondence between the plots and the respective Arabidopsis gene identification designation. The numerical key for each array experiment is given along the X-axis and the detail can be found in Additional file 1. Here is a brief list of the stress treatments: 1–18, control; 19–30, cold; 31–42, osmotic; 43–54, salt; 55–68, drought; 69–80, genotoxic; 81–92, oxidative; 93–106, UV-B; 107–120, wound; 121–136, heat; 137–141, cell culture control; 142–149, cell culture + heat.

Arthur G Hunt, et al. BMC Genomics. 2008;9:220-220.
8.
Figure 1

Figure 1. From: Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling.

Meta-analysis of Arabidopsis poly(A) factor gene expression during development. Normalized expression data for the NASC Arabidopsis developmental series (Additional file 1) were extracted and plotted as shown. The set of genes listed in Table 1 were split into three groups; the grouping was done according to historical views of the polyadenylation complex. Thus, genes encoding CPSF and CSTF subunits are shown in the top panel, PAPS and PABN genes in the middle, and the remaining genes in the lower panel. This grouping also applies for the plots shown in Figures 3–5. The legends indicate the correspondence between the plots and the respective Arabidopsis gene identification designation. The numerical key for each array experiment is given along the X-axis. The full list of the keys can be found in the Additional file 1. Here is a brief description of these samples, including wt and some mutants: 1–7, root 7–21 days; 8–10, stem 7–21 days; 11–27, leaf 7–35 days; 28–38, whole plant 7–23 days; 39–49, shoot apex 7–21 days; 50–71, flowers and floral organs 21+ day; 72–79, 8 week seeds and siliques. The arrows point to the positions for mature pollen.

Arthur G Hunt, et al. BMC Genomics. 2008;9:220-220.

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