Edit Gene Information Settings

The Gene Information Settings window allows you to define how the data you have imported into your project should be used.

Access the Gene Information Settings dialog by selecting Data > Gene Information Settings, or by clicking the Modify Gene Information Settings tool modify gene info settings button

from within the Set List or Advanced Filtering dialog.

The fields listed in this window will vary, based on the data you have imported into your project.

Select from the Gene name dropdown list the column from your data to be used by ArrayStar as the gene name. The data from the column you designate will be used as the gene name in the three graphical views where individual gene data are displayed: the Scatter Plot, the Heat Map, and the Line Graph views. The gene name is also used when exporting a set from your project.

You may also assign another column to be used as a Backup gene name, for example, if there are synonyms available in an imported annotation file. If data are not available for the column you specified to use as the Gene name, ArrayStar will use data from the field you specified in the Backup gene name dropdown list.

If “Any” is selected for either the Gene name or Backup gene name fields, ArrayStar will use the first field selected in the Display Gene Information section of the window.

The Display Gene Information section of the window allows you to choose the fields that you would like displayed as well as the order in which they are shown. These settings are reflected in the Genes pane of the Set List view, the Advanced Filtering Search Results pane, and in the Details section of the Info Pane for the Scatter Plot, Line Graph, and Heat Map views.

Select the fields to be displayed by checking the checkbox next to each field name.

Note: Choosing to hide and display fields from the Gene Information Settings dialog also affects the fields that are included should you choose to export genes from a graphical view.

To change the order in which the items will be displayed, select an item by clicking on it to highlight it, and then use the arrows on the right side of the window to move the item up or down. After making your selections, click OK.

The Field Formatting section in the bottom half of the window allows you to customize how the information in each annotation field is used and displayed.

• Primary delimiter: If an annotation field contains a delimiter, you can enter the delimiter string here so that each identifier within the field is separated.

• Secondary delimiter: If an annotation field contains more than one piece of information for each identifier, there may be a secondary delimiter. Enter the secondary delimiter string here in order to separate the information for each identifier.

• ID Index: If a secondary delimiter is specified, you may use the ID Index to specify which string should be used as the identifier for the term. If 1 is indicated, the first string will be used. If 2 is indicated, the second string will be used, and so on.

description of ID1 // ID1 // information regarding the source of ID1 /// description of ID2 // ID2 // information regarding the source of ID2 ///

Where /// is the primary delimiter, // is the secondary delimiter, and 2 is the ID Index. When you view this annotation field, ID1 and ID2 will be displayed, and the additional information can be viewed by hovering your mouse over the term.

• Gene Ontology ID Index: If an annotation field contains Gene Ontology identifiers, then the Gene Ontology ID Index may be used to specify which part of the term should be used as the Gene Ontology ID.

go_component: nucleus [goid 0005634] [evidence IEA]; go_function: DNA binding [goid 0003677] [evidence IEA];

Where ; is the primary delimiter and [ is the secondary delimiter. Since the Gene Ontology ID is separated by the secondary delimiter [, the Gene Ontology ID Index in this case would be 2.

• URL: If an annotation field contains information that you would like to use to link to a URL, you may specify the necessary URL formatting in this field. The string must be formatted with “{index}” in the URL wherever the identifiers should go.

…and you would like to link each ID to its page on NCBI’s website, you might provide a URL like this one, which uses the first two letters in one location and the numerical value in another:

This formatting would enable you to click on the term Mm.21874 and be linked to: