Signal Transduction


Supplemental Tables

 

Additional file 1: Table 1
Title of data: SUCAST SAS showing differential expression in response to the applied treatments.
The table lists all SAS whose expression was enriched or decreased in both biological samples for each experimental point. The plus sign indicates that the SAS expression is up-regulated, the minus sign indicates that the gene expression is down-regulated. The asterisk indicates that the SAS identity was not confirmed by re-sequencing. The table also shows the expression profile of these genes in six sugarcane tissues (**revised from [27]). The last four columns indicate the SOM groups in which these SAS were included (numbered according to Figure 1). The expression data for sugarcane tissues were inferred from microarray hybridizations of tissue samples against a common reference constituted by an equimolar mixture of the tissues sampled [27]. FL = flowers, LB = lateral buds, LV = leaves, RT = roots, IN1 = first internodes, IN4 =fourth internodes, PD = phosphate deficiency, H = inoculation with Herbaspirillum spp., GD = inoculation with Gluconacetobacter diazotrophicus.


Additional file 2: Table 2
Title of data: Log2 ratios of microarray signals between the Cy3 and Cy5 channels.
Description of data: For each clone, the median intensity value of the technical replicates was used to calculate the ratio between the experimental samples and the reference sample. The numbers 1 and 2 denote the different biological samples used for each experiment. The asterisk indicates that the SAS identity was not confirmed by re-sequencing. Only valid values are shown, excluding data from saturated, low-intensity and low-quality spots. Data from clones for which PCR reactions produced low yields or multiple bands were also removed. The table contains 1,555 elements and not 1,545. This is due to the fact that some SAS are represented more than once in the Table. This occurs when the same SAS is represented in more than one position in the 384-well plates and some of these positions did not have their identity validated by re-sequencing. In these cases, we opted to analyze these data separately.


Additional file 3: Table 3
Title of data: SUCAST protein kinases showing differential expression in response to the applied conditions.
For SAS included in the SOM clustering analysis, the group to which the SAS belongs is indicated. The plus sign indicates that the SAS expression is up-regulated, the minus sign indicates that the gene expression is down-regulated. The asterisk indicates that the SAS identity was not confirmed by resequencing. The last four columns indicate the SOM groups in which these SAS were included (numbered according to Figure 1). PD = phosphate deficiency, H = inoculation with Herbaspirillum spp., GD = inoculation with Gluconacetobacter diazotrophicus.


Additional file 4: Table 4
Title of data: Components of the SOM groups generated for ABA treatment.
Description of data: The table indexes all genes that were included in the clustering analysis (correlation coefficient >= 0.7 between the expression profiles obtained for the two biological replicates of a particular experiment) and their respective groups. The asterisk indicates that the SAS identity was not confirmed by re-sequencing.


Additional file 5: Table 5
Title of data: Components of the SOM groups generated for MeJA treatment.
Description of data: The table indexes all genes that were included in the clustering analysis (correlation coefficient >= 0.7 between the expression profiles obtained for the two biological replicates of a particular experiment) and their respective groups. The asterisk indicates that the SAS identity was not confirmed by re-sequencing.


Additional file 6: Table 6
Title of data: Components of the SOM groups generated for phosphate deficiency treatment.
Description of data: The table indexes all genes that were included in the clustering analysis (correlation coefficient >= 0.7 between the expression profiles obtained for the two biological replicates of a particular experiment) and their respective groups. The asterisk indicates that the SAS identity was not confirmed by re-sequencing.


Additional file 7: Table 7
Title of data: Components of the SOM groups generated for drought treatment.
Description of data: The table indexes all genes that were included in the clusteringanalysis (correlation coefficient >= 0.7 between the expression profiles obtained for the two biological replicates of a particular experiment) and their respective groups. The asterisk indicates that the SAS identity was not confirmed by re-sequencing.
** The two different results obtained for this SAS are related to different positions in the 384-well plates. In bothpositions the SAS identity was not validated by re-sequencing. Because of this, these positions were treated separately.


Additional file 8: Figure 1
Title of data: Neighbor-joining (NJ) tree of kinase domains from sugarcane protein kinases.
Description of data: Selected kinase domains were aligned to construct a distance tree with the NJ algorithm. Bootstrap values greater than 50% (500 replicates) are shown for nodes in the tree. The RLKs/RLCKs group is highlighted in gray and only some representatives of this group are included. The undefined kinases are highlighted in red. Drivers are in italic. The SAS name in the figure is preceded by a prefix based on the BLAST similarity searches as indicated in the Annotation Box. The branch color indicates the presence of additional Pfam [46] domain besidesthe pkinase domain as indicated in the Domains Box.


Additional file 9: Figure 2
Title of data: Neighbor-joining (NJ) tree of kinase domains of sugarcane RLKs and RLCKs.
Description of data: Selected kinase domains from sugarcane RLKs and RLCKs and from other plants (drivers) were aligned to construct a distance tree with the NJ algorithm. Bootstrap values greater than 50% (500 replicates) are shown for nodes in the tree. Drivers are in italic. Undefined RLKs and RLCKs are highlighted inred. The SAS name in the figure is preceded by a prefix based on the BLAST similarity searches as indicated in the Annotation Box. The branch color indicates the presence of additional Pfam [46] and SMART [47] domains besides the pkinase domain as indicated in the Domains Box.


Additional file 10: Table 8
Title of data: Sugarcane genes and primers selected for real-time PCR experiments.
Description of data: Primers were designed using the Primer Express 2.0 Software (Applied Biosystems) and BLAST searches against the SUCEST database were conducted to ensure the specificity of the selected primers. The column Experimental Datapoints lists the samples analyzed. Primer sequences for endogenous references were retrieved from [35] and [48]. The P value is the probability Pr(sample > reference) and Pr(sample < reference) for up- and down-regulated genes, respectively. The expression profile was considered validated when P >= 0.99.


Additional file 11: Table 9
Title of data: PCA analysis for defining the number of groups in SOM.
Description of data: The difference between the magnitude of principal component eigenvalues for each treatment (columns) estimates how many groups are minimally necessary in each SOM grouping analysis. When the difference is near zero, there is no substantial information added by increasing the number of seed groups in SOM.