Genes Window


The Genes window shows each entry of a genes database file. See the file formats page for details about this file. Each entry is shown in three parts:

  1. The primary gene symbol.
  2. The primary gene name.
  3. A list of secondary gene names. These are also known as 'aliases' for the gene, and may consist of other symbols or names for the gene, or for the proteins associated with the gene.
The Genes window display is synchronized to the Proteins window display. Whenever a protein entry is displayed in the Proteins window, a proteins to genes database 'links' file is searched to find the primary gene symbols which are associated with that protein, if any. Then a genes database file is searched for the first of these primary gene symbols. If that gene symbol is found, the primary gene name and the secondary gene names for that primary symbol are also displayed. The proteins to genes links file is also searched for all of the primary protein symbols which are associated with the first primary gene symbol, if any. These primary protein symbols are then displayed in the text field at the bottom of the window. One of these primary protein symbols should be the same as the primary protein symbol also displayed in the Proteins window.

Reading genes files

To read a genes database file, click the 'Read Genes...' button. Navigate through the Mac file system using the Open dialog, and choose a file to read. The file will be read and parsed, and all gene entries stored in memory. You must also read a proteins to genes links file in order to search the genes database.

Reading protein/gene links files

To read a protein/gene links file, click the 'Read Links...' button. Navigate through the Mac file system using the Open dialog, and choose a file to read. The file will be read and parsed, and all protein to gene entries stored in memory. See the file formats page for details about this file.

Finding multiple gene entries

The protein/gene links file may contain more than one primary gene symbol for a given protein. If this is the case, all primary gene symbols for the protein are displayed in red, separated by semi-colons. The primary gene name and secondary gene names for the first of these symbols is also displayed, if it occurs in the genes database file. To display the primary and secondary gene names for one of the other primary gene symbols, select one or more characters of another symbol in the text field (or just double click on the symbol), and click the 'Find Selected Gene' button. The primary and secondary gene names for that primary gene symbol will then be displayed, if it occurs in the genes database file.

Finding multiple protein entries

The protein/gene links file may contain more than one primary protein symbol for a given gene. If this is the case, all primary protein symbols for the gene are displayed in red, separated by semi-colons. To display protein database entry information for one of these primary protein symbols, select one or more characters of a symbol in the text field (or just double click on the symbol), and click the 'Find Selected Protein' button. The proteins database will then be searched for the selected symbol, and its entry information displayed in the Proteins window.

Selecting the font

All of the gene display fields are editable so that you can change their fonts. Changes to any of these fields are not written to the genes database or links files. To change the font of any of the gene text fields, click the mouse in the field and choose 'Select All' from the Edit menu. You can then access the Font menu and change the font with 'Show Fonts' or any of the other menu items. Only if you selected the entire text field will changes to the font persist to text in other gene entries.

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İSky Coyote 2002