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About the Gene Sorter

This program displays a sorted table of genes that are related to one another. The relationship can be one of several types, including protein-level homology, similarity of gene expression profiles, or genomic proximity.

To display a gene and its relatives:

  1. Select a genome and assembly from the corresponding pull-down menus.
  2. Type a word or phrase into the search text box to specify which gene should be displayed in the Gene Sorter. Examples of search terms include FOXA2, HOXA9, and MAP kinase.
  3. Choose the gene relationship with which you would like to sort the list by selecting an option from the sort by pull-down menu.
  4. Press the Go! button to display your results.

Following a successful search, the Gene Sorter displays a table containing the specified gene -- highlighted in light green -- and its relatives, each on a separate line. To adjust the number of rows shown, select an option from the display pull-down menu.

The default set of table columns -- which can be expanded, reduced, and rearranged via the configure button -- shows additional information about the genes. Some of the column data, such as those in the BLAST E-value and %ID columns, are calculated relative to the highlighted gene. To select a different gene in the list, click on its name. Clicking on a gene's Genome Position will open the UCSC Genome Browser to the location of that gene. Similarly, clicking on a gene's Description will open a page showing detailed information about the gene.

One of the most powerful features of the Gene Sorter is its filtering capabilities, accessed via the filter button. Use the filter to fine-tune the list of displayed genes to a subset based on a selection of detailed and flexible criteria. For example, the filter may be used to select all human genes over-expressed in the cerebellum that have GO-annotated G-protein coupled receptor activity.

The Gene Sorter offers two options for displaying and downloading sequence associated with the genes in the table. Clicking on the sequence button will fetch associated protein, mRNA, promoter, or genomic sequence. To dump the table into a simple tab-delimited format suitable for import into a spreadsheet or relational database, click the text button.

The UCSC Gene Sorter was designed and implemented by Jim Kent, Fan Hsu, Donna Karolchik, David Haussler, and the UCSC Genome Bioinformatics Group. This work is supported by a grant from the National Human Genome Research Institute and by the Howard Hughes Medical Institute.