Gene Report Help Page

1. Gene report pages can be accessed from the RGD front page in several ways. One can type a case-insensitive gene symbol or name into the “Search Term” box and press enter or click the magnifying glass icon, or click on “Genes” in the “Data” pulldown in the black toolbar, or on “Genes” in the light blue Search bar.

2. The “Search Term” method leads to an intermediate results page displaying objects in any of the ten RGD species, ontology terms or references containing the search query. Clicking on any highlighted number or phrase links to a list of matches for that category. To view the list of rat genes that match query “tnf”, click the “82” under “Rat” and see #5.

3. The second two gene search methods described in #1 link to the Gene Search page, where one can type in gene symbols, names or ID numbers, as indicated in the examples, and press “Enter” or click “Search Genes”.

4. The search can also be limited by chromosome, start and stop base pair coordinates and species, with rat as the default.

5. The search result for this, and from #2 above, is a results page of genes matching the search term (highlighted in yellow), with matching alleles, protein-coding regions, pseudogenes and splice variants (not shown) also accessible in the Filters at the left. Each gene is displayed with additional information explained in the blue bar at the top of the list. Multiple genes may be selected with the check boxes to the left of the gene symbols and downloaded or analyzed with RGD tools using links at the far right.

6. The search can be limited to a particular genome assembly, can be sorted by different parameters, and can be viewed by page or number of results.

7. Clicking the gene symbol links to that gene’s report page. All object report pages at RGD have a format similar to that of the gene report page.

8. Gene Symbol, Name and Species and Gene Page Tabs: The official gene symbol, official gene name and species name and species picture are prominently displayed at the top of the gene page. On the left side is a floating outline of the report page sections and subsections, with the one currently being viewed highlighted in dark blue. These can be accessed directly by clicking the section title or by scrolling down. The “General” tab is selected by default and contains most of the information in RGD about the gene. For genes with microarray IDs a second tab appears next to the “General” tab. The “Array IDs” tab contains lists of microarray probe IDs associated with the gene. Currently RGD imports probe to gene associations from Affymetrix and Ensembl. Probe lists are separated according to the source.

9. Description: An automated, current synopsis of specific gene information, based on annotations of the function, processes, pathways, cellular location, diseases, phenotypes and chemical interactions associated with the gene/gene product. The information may be either experimentally derived or inferred from rat, mouse or human orthologs.

10. Type: A one-word description to designate the gene as protein-coding, pseudogene, etc. If the gene report represents a splice variant or an allele, a link to the parent gene page will be included.

RefSeq Status: A one-word code related and linked to the NCBI RefSeq record and the GenBank sequence data that were used to provide the record.
Also known as: Symbols and synonyms that are also used or have been used to refer to this gene.