Searching RGD

Jump to information about the:

Keyword Search
RGD Search Result
Object Lists
Ontologies Search
Search by Position

 

For more about what terms you can use to search RGD and what data is searched, click here.

 

Keyword Search

1. General searches are performed by entering text into the 'Keyword' box in the upper right corner of every page.

2. An alternate way is to access the 'Search RGD' entry page by clicking 'Search RGD' on the home page.

3. Then text is entered into the 'Search RGD By Keyword' box.

4. Examples of the types of entries that can be made are given.

5. One can also search by position, entering chromosome number and base pair coordinates (see Position Search Result below).

6. An extensive list of search features is provided by clicking 'Listing of Search Features'.  One can also download various categories of data from the RGD FTP site link.

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Search Result

The results of a "Search RGD By Keyword' search, here for 'blood pressure', will be listed in two sections.

1. The first section, 'RGD Search Result', lists records found containing annotations with the search term. 

2. The RGD Search Result lists records found sorted by species into Genes, QTLs, Strains, SSLPs (not shown here) and References.

3. More detailed lists of objects in each category can be reached by clicking the 'View [Species] [Objects] Report' links in each section.

 

4. Alternatively, the numbers of records in each category summarized in the 'Result Matrix' table also link to these lists.

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Search Result/Object Lists

1. Clicking on 'View Rat Genes Report' (3 in RGD Search Result above) provides a list of gene records containing the search term (bold).

2. The list is tabbed for each species and is exportable (see below).

3. Descriptive information is presented in columns – the gene symbol links to the gene report page.

4. Search results can be filtered by genome assembly or by chromosome, and it is sortable by any column heading.  Additional searches for the specific data object and species can be performed from this page by entering a different or additional term in the "Refine Term" box and clicking "Update".  Search results for other objects such as QTLs and strains, are configured similarly.

Search results can be exported in a number of ways.  "CSV" and "TAB" both export the data as tab-delimited text files which can be opened in Excel or another spreadsheet program for further analysis; "Printer" sends the results to the default printer to create a hard-copy record of your search results; "Genome Viewer" sends the results to the RGD GViewer genome viewer tool, giving you a genome-wide view of your search results against the chromosomes of the corresponding species.  Although this is not available from the "All" tab, it is accessible for rat, mouse and human.  For more about the GViewer tool, click here.

 

 

 

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Ontologies Search Result

1. The second results section of a "Search RGD By Keyword' search is called 'Ontologies'; it lists ontology terms containing the search term, organized by ontology.

2. Clicking on a term links to the ontology report page for that term. A boxed 'A' following the term indicates that there are annotations to it.

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Position Search Result

1. The results of a 'Search RGD By Position' search (5 in Keyword Search above) is a table of the numbers of genes, SSLPs and QTLs in the specified region.

2. This is followed by a complete list of all of those objects, giving the RGD ID, linked to the object report page, the object type, symbol, name, chromosome number, and start and stop coordinates.

3. The tables are exportable to a spreadsheet.

4. The lists are separated by object type, followed by a list of all objects together.

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