To initiate a search for correlation between two sets of genes, select the Analysis>Correlations>Get correlations between genes command on the main menu. The Correlation analysis setup wizard will assist you with setting up search parameters.
Select two sets from the total number of genes: Set 1 that corresponds to the rows of the correlation matrix and Set 2 that corresponds to the columns of the correlation matrix. These sets of genes may overlap. The pairwise correlation coefficients are calculated for the expression profiles of genes from these sets. As a result, the program creates an n*m correlation matrix, where n is the number of rows and m is the number of columns. The matrix element (i,j) corresponds to the correlation coefficient between the expression profiles of the ith gene from Set 1 and the jth gene from Set 2.
In the first wizard box (Fig. 3.7.1), you can define the following two sets from the total number of genes:
3.7.1. The "Set 1 (rows)" list contains genes that comprise Set 1. Click "Mark all" to select all genes in the list and "Unmark all" to unselect all genes in the list.
3.7.2. The "Set 2 (columns)" list includes genes that will comprise Set 2. Click "Mark all" to select all genes and "Unmark all" to unselect all genes in the list.
To proceed, click "Next"; to cancel the operation, click "Cancel".
Figure 3.7.1.
1. The Set 1 list of genes. 2. The Set 2 list of genes. 3. The "Mark all" button that selects all genes in the "Set 1" list. 4. The "Unmark all" button that deselects all genes in the "Set 1" list. 5. The "Mark all" button that selects all genes in the "Set 2" list. 6. The "Unmark all" button that deselects all genes in the "Set 2". 7. The "Next" button that takes you to the next wizard box. 8. The "Cancel" button that cancels the calculations.
The second box of the Correlation analysis setup wizard (Fig. 3.7.2) allows you to define values for the following parameters:
Figure 3.7.2.
1. The "Field" button that provides access to the "Field selection" dialog box. 2. List of correlation types. 3. List of threshold types. 4. The threshold value input field. 5. The "Back" button that takes you to the previous wizard box. 6. The "Finish" button that allows you to finish working with the wizard and start calculations. 7. The "Cancel" button.
3.7.3. The "Fields..." button calls the "Field selection" dialog box (see section 3.3 about the "Field selection" dialog box). The text field displays the number of selected fields.
3.7.4. The "Correlation type" list contains the following three types of correlation coefficients:
3.7.5. The "Threshold type" list contains four types of restrictions on gene selection (the matrix elements that exceed the threshold value are shown in red):
3.7.6. In the "Threshold value" field, set the value of the correlation threshold (see section 3.4.5). To finish working with the wizard and assess the correlation, click "Finish". To move to the previous wizard box, click "Back"; to cancel the operation, click "Cancel".
Note. 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. 3.7.3).
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When the calculation is in progress, you will see the "Please wait" information box (Fig. 3.7.4) that will disappear after the calculation is complete.
Figure 3.7.4 "Please wait" information box.
After the program completes the calculation, it will open a dialog box with the correlation matrix (see section 3.9 about this dialog box).