...
The basic method of creating a gene list from ANOVA results based on fold-change and p-value cut-offs is detail in detailed in Creating gene lists from ANOVA results. Advanced options enable the creation of lists based on more complex criteria. For example, we can use the Create Gene List function to identify transcripts that are both significantly differentially expressed AND alternatively-spliced among the four tissue samples.
...
Numbered figure captions |
---|
SubtitleText | Configuring criteria for transcripts with a p-value < 0.05 |
---|
AnchorName | Configure Criterea |
---|
|
Image RemovedImage Added |
- In the Configure Criteria dialog box (Figure 2), provide a name for the list (Diff Exp)
- Select 1/transcripts (RNA-Seq_results.transcripts) from theSpreadsheet drop-down menu
- Select 8. p-value(DiffExp) from the Column drop-down menu
- Set Include p-values to significant with FDR with a value of 0.05
A list of 3038,305 285 transcripts that pass this criteria will be generated according to the # pass score on the right-hand side of the dialog. If the settings are changed, this number will automatically update.
...
Numbered figure captions |
---|
SubtitleText | Configuring criteria for a list of alternatively spliced genes |
---|
AnchorName | Configuring Gene List another |
---|
|
Image RemovedImage Added |
- Select OK to generate Alt Splice
- Select both lists in the right-hand panel under the Criteria panel while holding the Ctrl key on your keyboard
- Select Intersection from the left-hand panel of the List Manager dialog (Figure 4)
Numbered figure captions |
---|
SubtitleText | Creating a gene list at the intersection of two criteria |
---|
AnchorName | Creating an Intersection Gene List |
---|
|
Image RemovedImage Added |
- Enter a name for the criteria (Diff Exp and Alt Splice)
- Select OK to close the naming dialog and OK again to close the list creation hint dialog
- Select Save List from the Manage criteria section of the List Manager dialog (Figure 5)
Numbered figure captions |
---|
SubtitleText | Saving a created list criteria |
---|
AnchorName | Saving Created List |
---|
|
Image RemovedImage Added |
- Select Diff Exp and Alt Splice in the List Creator dialog (Figure 6)
Numbered figure captions |
---|
SubtitleText | Selecting list to save in List Creator dialog |
---|
AnchorName | List Creator dialog |
---|
|
|
- Select OK to save the list
- Select Close to exit the List Manager dialog and view the Diff_Exp_and_Alt_Splice spreadsheet (Figure 7)
Numbered figure captions |
---|
SubtitleText | A list of the differentially expressed and alternatively spliced genes is now available for downstream analysis |
---|
AnchorName | Viewing Created List |
---|
|
Image RemovedImage Added |
This list of differentially expressed and alternatively spliced transcripts will be used later in the next section of the tutorial.
...