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Meaning

Click the Choose Quick-Filter tool to filter data based on any of the following.

•      Show All ____ – Displays all instances of this item (e.g., genes, SNPs, exons) in the project.

•      Show Only Selected ____ – Displays only the globally-selected items chosen via the Select in all views tool (see below). The selection is independent of the rows currently selected in the table.

•      Show Only _____ Set – Displays only the items in a specified set (e.g. of genes, SNPs, etc.). If you choose this option, a dialog launches with a list of available sets.

The following options are only available in the SNP Table:

•      Show SeqMan NGen Default SNPs – For .assembly files, displays only SNPs that meet the SNP stringency criteria specified in SeqMan NGen prior to assembly. For some targeted workflows, SeqMan NGen sets the filter to include only those SNPs located in targeted regions, by default. To learn how to view additional SNPs in the SNP Table, see View Variants Outside Targeted Regions.

•      Show Only User SNPs – Displays only SNPs included in the user-defined custom VCF SNP file chosen within the SeqMan NGen wizard. This option does not refer to VCF files imported directly into ArrayStar.

•      Show Only Coding Region SNPs – Displays only SNPs located in coding regions.

•      Show Only Non-synonymous SNPs – Displays only SNPs that alter the encoded amino acid sequence in a coding region.

•      Show Only Gene-disrupting Variants – Displays only SNPs that result in a premature stop codon.

Click the Edit Notes tool to add or edit notes for the currently selected item (e.g., gene, SNP, etc.).

Click the Copy Selected Table Rows tool to place the selected data on your clipboard. For ontology terms, a “GO ID” column is added to the table and includes each relevant term ID from the Gene Ontology Consortium. If you would like to obtain an unformatted copy of the selected table cells, hold down the Ctrl+Shift+Alt keys while clicking the tool.

Click the Print tool to print the table.

Click the Print Preview tool to view the table on your screen as it will appear on the printed page(s).

Click the Export Selected Table Rows tool to export the data in the currently highlighted rows as a tab-delimited or comma-delimited text file.

Click the Add/Manage Columns tool () to add new columns for any of the experiments in your project (see Using the Manage Columns Dialog). For detailed information about each available column type, see Table Column Descriptions.

Click the Add Fold Change tool to display the fold difference between a pair of experiments. Clicking the tool will display a dialog, asking you to select from a dropdown list the control and experiment between which to calculate the fold change.

Click the arrow to the right of the Select in All Views tool and choose from the available options, which vary depending on the table type:

•      Select in All Views –To create a new global selection from the currently highlighted genes in the table.

•      Select and Remember as a _____ Set – To use the highlighted genes to create a new set of genes, SNPs, exons, etc.

The following options are only available in the SNP Table:

•      Show the Genes for this SNP – To switch to the Gene Table and highlight the gene(s) there that correspond to the SNPs selected in the SNP Table.

•      Show the SNPs for this Gene – To switch to the SNP Table and highlight the SNPs for the corresponding genes that are highlighted/selected in the Gene Table.

Click the Add to Selection in All Views tool to add the currently highlighted genes in the Gene Table to the existing global selection.

Click the Remove from Selection in All Views tool to remove the currently highlighted genes in the Gene Table from the existing global selection.

In the SNP Table, click the Set Colors tool to access the Set Colors window.