ArrayStar
Scatter Plot
ArrayStar’s Scatter Plot view gives a visual comparison of gene expression levels between any two datasets; whether they are individual arrays or replicated sets. Each data point on the Scatter Plot represents an individual gene and is plotted based on its expression level in both of the selected experiments. Data can be scaled and visualized as either linear or log2 values.
Specific groups of genes of interest can be targeted easily. As the image shows, gene groups do not necessarily need to be adjacent on the plot to be selected. Selected genes are indicated in this view by being white in color.
Three solid green lines are drawn diagonally across the scatter plot. The middle green line is the identity line, or the x=y line. Data points on this line represent genes that are expressed at the same level in both datasets. The other two lines delineate genes with at least a two-fold change in intensity value in one of the datasets.
The dashed purple line on the scatter plot is the linear regression or “best-fit” line, a line that passes as near to as many data points as possible.
Each data point is colored to reflect where it is in comparison to the x=y line. The colors for data points, as well as the fold lines and regression line can be changed to match your preferences.
Info Pane
The Scatter Plot screen gives users additional valuable information besides what is shown on the graph. On the right side of the Scatter Plot is the Info Pane. This section provides statistical information for the data plotted on the Scatter Plot. Results of the use of either the Student's t-test or the Moderated t-test are shown in the display beneath the drop down box.
Comparisons of different data sets can easily be performed to examine expression changes at different experimental stages.
Statistical Tests
The Student’s t-Test is used to compare the means of gene expression values for two individual replicates or for two groups of replicates for a given gene. The Student’s t-Test is a widely used method for identifying differentially expressed genes.
The Moderated t-Test is similar to the Student’s t-Test in that it is used to compare the means of gene expression values for two individual replicates or two groups of replicates for a given gene. The primary difference between the two methods is in the calculation of variance. The Student’s t-Test calculates variance from the data that is available for each gene. The Moderated t-Test uses information from all of the selected genes to calculate variance. The Moderated t-Test is thought by some to be superior in this aspect.
Selecting a statistical test from the list will automatically generate:
Links showing different confidence levels The number of genes associated with that confidence level.
Fold Changes
Fold change can be valuable in identifying gene expression differences between control and treated samples that fall outside of the thresholds. During the analyses researchers frequently want to examine the effect of different fold changes on their data. Fold changes and confidence levels can be changed by the user if desired. Links showing various fold changes and the number of genes meeting that threshold are also listed.
Filtering
Advanced filtering techniques can be applied to the selected genes. This allows users to further refine their search. Users can either filter all of the genes in a project or only the genes that are currently selected.
Search criteria available to users are:
Gene Annotations Expression Level Fold Change Statistics
Gene Details
The Detail section of Info Pane provides users with information on the number of genes selected. Passing the cursor over any individual gene brings up gene ontology information, expression levels for the 2 different days graphed, fold change, p-values and t-values.
When no genes are highlighted, the section shows users the total number of genes in the experiment, the XY coordinates for the scatter plot and the scale used in the plot.
Action Area
The bottom section of the panel is an Actions area. This is designed to prompt users regarding possible next steps they may want to perform in the analysis. The Actions section of the Info Pane is only visible when a selection of data has been made on the Scatter Plot. When any selection is made, several options appear for the user to consider:
perform a hierarchial clustering with the selected genes, perform a k-Means clustering with the selected genes, remember the selected gene set show a table of the selected genes.
Gene Set Export
Any group of genes selected on the scatter plot can be exported from the view as a tab-delimited.txt file.
Scatter Plot Print
The scatter plot can easily be printed and previewed prior to print.