This feature is accessed from the Analysis>Correlations>Select most correlated genes command on the main menu. To specify the parameters of your query, follow the procedure organized as wizard boxes.
The first wizard box (Fig. 3.6.1.1) helps you create selection lists.
3.6.1.1. A list of genes available for selection is titled "Gene list to select from." The list includes genes from the current table. You can enter a selection mask into the text filed above the gene list. In the mask, the "%" symbol substitutes any single symbol and "*" substitutes any number of symbols. In Figure 3.6.1, you can see the result of gene selection by mask.
3.6.1.2. A list of selected genes is titled "Specified genes (query set to compare with)". The list contains genes selected from list 3.6.1.1. You can enter a selection mask into the text field above the list. In the mask, the "%" symbol substitutes any single symbol and "*" substitutes any number of symbols.
A set of genes (Set 2) that can contain one or more genes is selected from list 3.6.1.1. Set 2 is displayed in list 3.6.1.2. Set 1 is the genes that remain in list 3.6.1.1. Sets 1 and 2 have no common genes.
3.6.1.3. Control buttons
"Add->" - Move the genes selected in list 1 to list 2.
"All->" - Move all genes from list 1 to list 2.
"<-Remove" - Move the genes selected in list 2 to list 1.
"<-All" - Move all genes from list 2 to list 1.
"File load'" - Import list 2 from a file. In this version of the program, this option is unavailable.
In Set 1, the program selects genes with expression profiles most similar to those of genes from Set 2. When you exit the dialog box, the program creates the expression profiles for selected genes and writes the correlation coefficients in a separate table.
3.6.1.4. If the "Initial gene set" checkbox is checked, the gene names from the initial table will be added to list 1, regardless of the current table.
To proceed with the operation, click "Next"; to cancel the operation, click "Cancel."
Figure 3.6.1.1.
1. Control buttons for managing the gene selection list and the selected gene list. 2. Gene selection list. 3. Selected gene list. 4. The checkbox that enables you to add genes from the main table to the gene selection list. 5. The "Next" button that allows you to move to the second wizard box. 6. The "Cancel" button.
In the next wizard box (Fig. 3.6.2.1), you can define values for the following parameters:
3.6.2.1. The "Fields..." button calls the "Field selection" dialog box (Fig. 3.3). The text field displays the number of selected fields.
3.6.2.2. The "Correlation type" list contains three types of correlation coefficients:
3.6.2.3. The "Threshold type" list contains four types of restrictions on gene selection:
3.6.2.4. In the "Threshold value" field, set the value of the correlation threshold (see section 3.6.2.3.).
3.6.2.5. The "Regime to treat multiple genes for query set" list offers three computation modes:
To finish working with the wizard and calculate the correlation, click "Finish". The program will create expression profiles for the selected genes and write the correlation coefficients in a separate table. To move to the next wizard box, click "Back"; to cancel the operation, click "Cancel".
Figure 3.6.2.1.
1. The "Field" button that calls the "Field selection" dialog box. 2. List of correlation types. 3. List of threshold types. 4. The threshold value input field. 5. Correlation modes. 6. The checkbox that allows you to view the correlation matrix in a separate window. 7. The "Back" button that takes you to the previous wizard box. 8. The "Finish" button that allows you to finish working with the wizard and perform calculations. 9. The "Cancel" button.
Notes. If the sets of genes have not been formed or calculation fields have not been determined, the "Error" information box with relevant messages will appear (Fig. 3.6.2.2).
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When calculation is in progress, you will see the "Please wait" information box (Fig. 3.6.2.3) that will disappear after the calculation is complete.
Figure 3.6.2.3 "Please wait" information box
Figure 3.6.3.1.
1. The table with the genes selected. 2. The name of the new table.
Figure 3.6.3.2.
1. The buttons for selecting the graphical representation type. 2. Profile view area. 3. Gene list. 4. Group list. 5. Information about the gene you are pointing to with your mouse.
Figure 3.6.3.3.
Figure 3.6.3.4.
1. Information about the number of fields and groups. 2. Group list. 3. The fields included into the selected group. 4. Information about the selected group.