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  • Invoke the List Manager dialog by selecting Create Gene List in the Analysis section of the Gene Expression workflow
  • Ensure that the 1/ANOVA-3way (ANOVAResults) spreadsheet is selected as this is the spreadsheet we will be using to create our new gene list as shown in (Figure 2419)
  • Select the ANOVA Streamlinedtab. In the Contrast: find genes that change between two categories panel, chooseDown Syndrome vs. Normal and select Have Any Change from the Setting dropdown menu list. This will find genes that have a fold change different between the types of samples
  • In the Configuration for “Down Syndrome vs Normal” panel, check that Include size of the changeis selected and enter 1.3 into Fold change >  and -1.3 in OR Fold change <
  • Select Include significance of the change, choose unadjusted p-value from the dropdown menu, and < 0.0005 for the cutoff. The number of genes that pass your cutoff criteria will be shown next to the # Pass field. In this example, 23 genes pass the criteria. 
  • Set Save the list as A, select Create, and then select Close to view the new gene list spreadsheet

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The plot will be divided into six sections. By clicking on the upper-right section, all genes in that section will be selected (Figure 25).

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Figure 25
Figure 25

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  • Specify a name for the gene list and write a brief description about the list (Figure 25). The description is shown when you right-click on the spreadsheet > Info > Comments

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