PMC

Architecture of SysNet software.

List of molecules that correlate with the molecule of interest. The left panel shows information for the molecule of interest. All correlated molecules are displayed in the right panel. By highlighting a molecule in the right panel, the user can either invoke another molecular window of the highlighted molecule by clicking the 'Show Element' button or invoke a correlation window by clicking the 'Show Correlation' button.

Graphic display of the same molecular correlations in (a) one circle and (b) heat map with high contrast color schema. High contrast color schema is used to show the correlation directions. Green indicates positive correlation while red indicates negative correlation. The encircled areas in panel (b) readily demonstrate clusters of strong molecular correlation.

Interactive display of molecular correlation in multiple circles with the normal SysNet color schema. The left panel displays molecular information and the right panel displays molecular correlations. Each circle represents elements measured in one Arabadopsis strain (i.e., in each experimental group). Col0 is a wild-type plant whereas Ler2, fpt2 and 152–54 are mutants.

Display of molecule behavior in a comparative analysis. The second comparative experiment labeled as DataSet 2 on the upper left panel is the active experiment group including the molecular expression levels of the molecule of interest (cadmium, Cd) in each sample displayed in the lower graphic panel. a) the expression levels of this element in samples 1 and 8 were detected as outliers and highlighted in red; b) the outliers in the active experiment have been removed by un-checking S1 and S8 in the left panel.

Correlation between two elements (Li and P) in the ler2 Arabadopsis strain. The information for the two correlating elements is displayed in the list boxes on the left. There are 12 ler2 ionomics samples. The middle graphic shows the expression data of the two elements, with the level of Li on the x-axis and P on the y-axis. Each point therefore represents the expression levels of Li and P in the same sample. Statistical correlation information is listed on the right side of the screen. The critical values for the correlation test are also displayed to facilitate assessment of the statistical significance of the selected correlation.

Comparative analysis of 'omics expression data. Molecules are aligned in concentric circles based on molecular name and experimental group. Experimental groups (sets) are displayed as concentric arcs of the circles with each circle representing a separate comparative experiment. Molecules indicated in red are identified in each experiment in the set. Molecules indicated in black were not identified in all comparative experiments. The outer most circle provides an index of every molecule detected in the comparative studies with a designated index number which can be used to find the relevant experimental and molecular information on the left panel lists. The user can interactively select or de-select molecules and experimental groups in the left panel, and the related information will be automatically displayed in the graphic.