2.2. Main menu commands and toolbar buttons
- The "File" menu contains the following commands for file operations:
- "Open expression data" (Ctrl+O),
button - opens the "Open" dialog box, which allows you to load a file with a gene expression table.
- "Close expression data" (Ctrl+O) - unloads a file with a gene expression table.
- "Save as",
button - opens the "Save as" dialog box so that you can save the current data under a new name or in a new location.
- "Link sequence" - downloads a file with the nucleotide sequences of genes. Calls the "Load data" dialog box from where you can load a file. After the file is loaded, the "Show sequence" command on the shortcut menu becomes active.
- "Link gene data" - links a file with gene descriptions. Calls the "Load data" dialog box from where you can load a file with gene descriptions. After the file is loaded, the "URLs>UniGene" command becomes active on the shortcut menu.
- "Unlink sequence" - unlinks the selected file with nucleotide sequences from main data.
- "Unlink gene data" - unlinks the file with gene descriptions from main data.
- "Quit" - exits the program.
- The "Group" menu contains commands for managing groups of experiments:
- "View group" - calls the "View group data" dialog box, where you can view groups.
- "Add group" - calls the "Edit group data" dialog box from where you can create groups.
- "Edit group" - calls the "Select field group" dialog box. In this dialog box, you can select one group to be edited in the appropriate dialog box.
- "Delete group" - calls the "Delete field group" dialog box so that you can delete one (or several) groups.
- The "Table" menu contains commands for working with tables:
- "Select genes by query" - calls the "Make selection" dialog box. In this dialog box, you can select genes that satisfy specified conditions and create a new table for these genes.
- "Selections list" - calls the "Select table" dialog box, which allows you to select a table. This dialog box displays the main gene expression table that lists all the genes loaded when you started the current project and tables generated as a result of selections (Fig. 2.2.1).
- "Quick search gene in current selection" - calls the "Quick search" dialog box from where you can search for specific genes in a table by their field value.
- "Remove all generated selections" - removes all tables generated as a result of selections.

Figure 2.2.1 "Select table" dialog box.
1. List of tables. 2. The "Select" button. 3. The "Cancel" button.
- The "Analysis" menu contains a set of commands for data analysis:
- "Correlations":
- "Select most correlated genes" - calls the "Select most correlated genes for specified gene set" dialog box designed to search for genes whose expression profiles are best correlated with those of one or more genes.
- "Get correlations between genes" - calls the "Correlation analysis setup" dialog box, which allows you to calculate the correlation matrix between two sets of genes.
- "Get correlations between fields" - calls the "Correlation analysis setup" dialog box, which allows you to calculate the correlation matrix between two sets of fields.
- "Clustering":
- "Build gene tree" - calls the "Tree calculation setup" dialog box from where you can build a gene tree.
- "Find genes cluster" - calls the "Setup for clustering procedure" dialog box, which allows you to set the parameters for gene clustering.
- "Find gene cluster (Ben-Dor algorithm)" - calls the "Setup clustering procedure (Ben-Dor) for genes" dialog box from where you can set the parameters for gene clustering by the Ben-Dor algorithm.
- "Find gene cluster (SOM algorithm)" - calls the "Setup for self-generated clustering procedure" dialog box from where you can specify the parameters for gene clustering by the self-organizing maps (SOM) algorithm.
- "Build field tree" - calls the "Tree calculation setup" dialog box so that you can build a field tree.
- "Find field cluster (Ben-Dor algorithm)" - calls the "Setup clustering procedure (Ben-Dor) for fields" dialog box, which allows you to set the parameters for field clustering by the Ben-Dor algorithm.
- "Find field cluster (SOM algorithm)" - calls the "Setup for self-generated clustering procedure for fields" dialog box from where you can specify the parameters for field clustering by the self-organizing maps (SOM) algorithm.
- "Principal component" - calls the "Setup for principal component analysis" dialog box from where you can analyze the correlation and covariance matrices of gene expression profiles using the principal component method and visualize the results obtained.
- "Expression map" - opens the expression matrix map.
- "Profiles map" - opens the "Profile dialog" dialog box, which allows you to visualize the profiles of genes from the current table.
- The "Options" menu is unavailable in this version.
- The "Help" menu provides access to help topics.
- "About" - calls the "About SELTAGX" dialog box with information about the program (Fig. 2.2.2).

Figure 2.2.2 "About SELTAGX" dialog box