VANTED: A system for advanced data analysis and visualization in the context of biological networks-4

<p><b>Copyright information:</b></p><p>Taken from "VANTED: A system for advanced data analysis and visualization in the context of biological networks"</p><p>BMC Bioinformatics 2006;7():109-109.</p><p>Published online 6 Mar 2006</p><p>PMCID:PMC1413562.</p><p>Copyright © 2006 Junker et al; licensee BioMed Central Ltd.</p>east invertase in an inducible manner [33] were mapped onto nodes before a correlation analysis was performed. See legend of Figure 3 for details on the diagrams. Positive and negative correlations are visualized by blue and red edges, respectively. The intensity of the edge depends on the value of Pearson's product-moment correlation coefficient. A combination of circular and force-directed layout was performed for better visualization. On the side-panel, a scatter plot is shown for the four metabolites that are marked with the small red squares in the network. Samples are color coded depending on the plant line. In the status bar, information is displayed concerning the correlation edge that is marked with yellow squares in the network (between D-Fructose 6-phosphate and D-Glucose 6-phosphate)

VANTED: A system for advanced data analysis and visualization in the context of biological networks-3

<p><b>Copyright information:</b></p><p>Taken from "VANTED: A system for advanced data analysis and visualization in the context of biological networks"</p><p>BMC Bioinformatics 2006;7():109-109.</p><p>Published online 6 Mar 2006</p><p>PMCID:PMC1413562.</p><p>Copyright © 2006 Junker et al; licensee BioMed Central Ltd.</p>nzymes present in the model plant as predicted from sequence information are shown in green. Selected enzyme activities and metabolite concentrations from wildtype potato tubers, and tubers expressing a yeast invertase either in an inducible or constitutive manner [33] were mapped on the pathway (which for better visualization was slightly modified using the built-in graph editor of VANTED). See legend of Figure 3 for details on the diagrams. The number of matches between the data set and all KEGG pathways is shown in the first number next to the pathway entry. The second number shows the number of enzymes in a pathway, the last the total number of nodes in the pathway (enzymes, metabolites, and links to other pathways)

VANTED: A system for advanced data analysis and visualization in the context of biological networks-5

<p><b>Copyright information:</b></p><p>Taken from "VANTED: A system for advanced data analysis and visualization in the context of biological networks"</p><p>BMC Bioinformatics 2006;7():109-109.</p><p>Published online 6 Mar 2006</p><p>PMCID:PMC1413562.</p><p>Copyright © 2006 Junker et al; licensee BioMed Central Ltd.</p>ost anthesis and analyzed for the dynamical changes of several central metabolites. The data set was mapped onto a network that was previously created in VANTED. Each node represents a metabolite, connected by solid and dashed lines that represent single and lumped enzyme reactions, respectively. Data are means of two independent plants, the standard error of the mean (SEM) is shown as a polygon around the line. A self-organizing map algorithm was performed to cluster the metabolites into three groups by similar behavior over time, which is visualized by the background color

VANTED: A system for advanced data analysis and visualization in the context of biological networks-2

<p><b>Copyright information:</b></p><p>Taken from "VANTED: A system for advanced data analysis and visualization in the context of biological networks"</p><p>BMC Bioinformatics 2006;7():109-109.</p><p>Published online 6 Mar 2006</p><p>PMCID:PMC1413562.</p><p>Copyright © 2006 Junker et al; licensee BioMed Central Ltd.</p> wildtype potato () tubers, and tubers expressing a yeast invertase either in an inducible or constitutive manner [33] was mapped onto the network. Each node represents a metabolite, connected by solid and dashed lines that represent single and lumped enzyme reactions, respectively. Data are means +/- standard error of the mean (SEM) of six independent plants. Values significantly different from the wildtype control as determined by an unpaired -test (< 005) were automatically marked with an asterisk. The bars in each diagram from left to right represent the values for the wildtype control (red), six inducible invertase lines, and one constitutive invertase line (light pink). The picture was created in VANTED and saved as a PNG file

VANTED: A system for advanced data analysis and visualization in the context of biological networks-1

<p><b>Copyright information:</b></p><p>Taken from "VANTED: A system for advanced data analysis and visualization in the context of biological networks"</p><p>BMC Bioinformatics 2006;7():109-109.</p><p>Published online 6 Mar 2006</p><p>PMCID:PMC1413562.</p><p>Copyright © 2006 Junker et al; licensee BioMed Central Ltd.</p> file format, e.g. MS-Office Excel, Open Office and Gnumeric. Information about the experiment, a description of the genotypes or sample conditions, and finally the data values including replicate number, sample time, measuring tool, and unit may be filled in. The template is then imported into VANTED for data visualization and analysis

tpc129601_SupplementalData

Supplemental Data Set

AtRD22 and AtUSPL1, Members of the Plant-Specific BURP Domain Family Involved in <i>Arabidopsis thaliana</i> Drought Tolerance

<div><p>Crop plants are regularly challenged by a range of environmental stresses which typically retard their growth and ultimately compromise economic yield. The stress response involves the reprogramming of approximately 4% of the transcriptome. Here, the behavior of <i>AtRD22</i> and <i>AtUSPL1</i>, both members of the <i>Arabidopsis thaliana</i> BURP (BNM2, USP, RD22 and polygalacturonase isozyme) domain-containing gene family, has been characterized. Both genes are up-regulated as part of the abscisic acid (ABA) mediated moisture stress response. While <i>AtRD22</i> transcript was largely restricted to the leaf, that of <i>AtUSPL1</i> was more prevalent in the root. As the loss of function of either gene increased the plant's moisture stress tolerance, the implication was that their products act to suppress the drought stress response. In addition to the known involvement of AtUSPL1 in seed development, a further role in stress tolerance was demonstrated. Based on transcriptomic data and phenotype we concluded that the enhanced moisture stress tolerance of the two loss-of-function mutants is a consequence of an enhanced basal defense response.</p></div

Influence of drought stress treatment on single and double loss of function mutants.

<p>A) Four weeks old wild type (Col-0), single and double mutant plants (<i>rd22-1</i> and <i>uspl1, rd22-1/uspl1</i>) were drought stressed for 1–5 days before they were returned to climate chamber conditions. Time of stress treatment in days is indicated left. B) Growth rates of plants under control and drought stress conditions. Bars indicate the growth rates at 22 days after sowing (DAS) for early phase of drought stress and 34 for the late phase of drought stress. For application of drought stress stop of watering started at 21 DAS. Wild type (Col-0): green bar; <i>rd22-1</i>: bright blue bar; <i>rd22-2</i>: dark blue bar; <i>uspl1</i>: purple bar; <i>rd22-1/uspl1</i>pink bar. Original data: <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110065#pone.0110065.s005" target="_blank">Figure S5 B</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110065#pone.0110065.s009" target="_blank">Table S2</a>, Asterisks indicate significant differences (p<0.01). C) NIR reflection as a water content-related parameter. Bars indicate the NIR intensity at 21 days after sowing (DAS) for start of experiment and at 35 DAS for the end of experiment. Wild type (Col-0): green bar; <i>rd22-1</i>: bright blue bar; <i>rd22-2</i>: dark blue bar; <i>uspl1</i>: purple bar; <i>rd22-1/uspl1</i>pink bar. N_control = 5, N_stress = 10 plants. Original data in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110065#pone.0110065.s010" target="_blank">Table S3</a>.</p

Top differential expressed genes in A) <i>rd22-1</i> and B) <i>uspl1</i> at standard growth conditions in the aerial part of 2 week old seedlings.

<p>Complete list of differential expressed genes in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110065#pone.0110065.s011" target="_blank">Table S4</a>.</p><p>Top differential expressed genes in A) <i>rd22-1</i> and B) <i>uspl1</i> at standard growth conditions in the aerial part of 2 week old seedlings.</p

Histochemical <i>ProAtUSPL1::GUS</i> activity in transgenic Arabidopsis plants.

<p>The <i>AtUSPL1</i> promoter activity was determined by histochemical localisation of GUS activity derived from the transgenic <i>ProATUSPL1::GUS</i> reporter gene. Activity indicated by blue colour can be seen in A) seedling; B) in funiculus of mature seeds; C) in flowers and stems; and D) in roots.</p