GoMiner uses the databases provided by the GO Consortium. These databases combine information from a number of different consortium participants, include information from many different organisms and data sources, and are referenced using a variety of different gene product identification approaches. The current database version is 2011-01.
GoMiner and its supporting scripts include a number of different features to enhance and query the GO database to make it easier to integrate the results of user experiments. This page provides a summary of these enhancements and options. It also provides links to the more detailed descriptions and instructions for users to establish their own local copies of the GO database with these enhancements.
By default, the GoMiner GUI application will query data for information from all organisms and from all data sources. For a particular gene in the input file, GoMiner will search for matches from all of the data sources and organisms in the GO Consortium database to find matching entries, and will then report all of the gene category associations found for those matches. You may wish to restrict your search to particular organism(s), or to a particular data source(s). To do so, make your selections from the Organism and Data Source menus respectively, before you read in the total genes file. There are corresponding filters available on the command-line interface.
GoMiner has two ways that it can enhance the search for genes in the GO Consortium database: Cross Reference and Synonym. You may choose which approach you want with the Lookup Settings menu. This menu is activated after you have loaded the GO terms (File Menu). There are corresponding filters available on the command-line interface. You can use any of these lookup options, alone, or in combination, or none of them at all.
In addition to the identifiers found in the symbol column of the gene_product table, the GO Consortium database also provides a cross-reference table with additional identifiers. Like the symbol column, this cross-reference table includes many different types of identifiers. A complete list of the available identifier types can be found on the GO site. When the Cross Reference option is selected, GoMiner will search the symbol column for genes you submit, and as well as the cross-reference table. This feature is available using the regular distrubution of the GO Consortium database.
In addition to the identifiers found in the symbol column of the gene_product table, the GO Consortium database also provides a gene product synonym table with additional identifiers. Like the symbol column, this synonym table includes many different types of identifiers. When the Synonym option is selected, GoMiner will search the symbol column for genes you submit as well as the cross-reference table. This feature is available using the regular distribution of the GO Consortium database. This option is also useful if you are using yeast data with ORF identifiers.
This option is now obsolete. The GO Consortium database now contains HGNC gene symbols.
We used to have an option called "Original." This style of lookup is still available if you leave the lookup options, Cross Reference and Synonym unchecked.
For a number of reasons, you may find it helpful to install your own local copy of the database. Most users find that doing so improves GoMiner's performance substantially over using the database we provide on our discover server. We support local databases using MySQL. Some users are interested in updating their database more frequently than we update ours. Other users are interested in making their own customizations. This guide will help you choose the right database configuration. The MySQL installation is a bit more complex, and has additional documentation..
GoMiner™ is a development of the Genomics and Pharmacology Facility, Developmental Therapeutics Branch (DTB), Center for Cancer Research (CCR), National Cancer Institute (NCI).We would like to hear from you. You can reach the team via email.
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