...

In the plot, each dot is a sample of the original data. The Y-axis represents the log₂ normalized intensity of the gene and the X-axis represents the different types of samples. The median expression of each group is different from each other in this example. The median of the Down syndrome samples is ~6.3, but the median of the normal samples is ~6.0. The line inside the Box & Whiskers represents the median of the samples in a group. Placing the mouse cursor over a Box & Whiskers plot will show its median and range. 

...

...

The spreadsheet Down_Syndrome_vs_Normal (A) will be created as a child spreadsheet under the Down_Syndrome-GE spreadsheet.

This gene list spreadsheet can now be used for further analysis such as hierarchical clustering, gene ontology, integration of copy number data, or be exported into other data analysis tools such as pathway analysis.

You can practice creating new gene list criteria of your own to become familiar with the List Manager tool. For more information, you can always click on the (Image Removed) buttons.

Generating Gene Lists from a Volcano Plot

Next, we will generate a list of genes that passed a p-value threshold of 0.05 and fold-changes greater than 1.3 using a volcano plot.

...

...

In the plot, each dot represents a gene. The X-axis represents the fold change of the contrast (Down syndrome vs. Normal), and the Y-axis represents the range of p-values. The genes with increased expression in Down syndrome samples are on the right side of the N/C (no change) line; genes with reduced expression in Down syndrome samples are on the left. The genes become more statistically significant with increasing Y-axis position. The genes that have larger and more significant changes between the Down syndrome and normal groups are on the upper right and upper left corner. 

In order to select the genes by fold-change and p-value, we will draw a horizontal line to represent the p-value 0.05 and two vertical lines indicating the –1.3 and 1.3-fold changes (cutoff lines).

...

• Select OK to draw the cutoff lines
• Select OK in the Plot Rendering Properties dialog to close the dialog and view the plot

The plot will be divided into six sections. By clicking on the upper-right section, all genes in that section will be selected.

...

Note: If no column is selected in the parent (ANOVA) spreadsheet, all of the columns will be included in the gene list; if some columns are selected, only the selected columns will be included in the list.

• Specify a name for the gene list (example: volcano plot list) and write a brief description about the list. The description is shown when you right-click on the spreadsheet > Info > Comments. Here, I have named the list "volcano plot list" and described it as "Genes with >1.3 fold change and p-value <0.05" (Figure 14). 

 The list can be saved as a text file (File > Save As Text File) for use in reports or by downstream analysis software.

...