Today’s bioinformatics bite will lay the groundwork for a patron question that would be WAY too long for one post. One common objective in searching NCBI is to find all the information that you can about a particular gene. To do this, you need to have 2 basic pieces of information:
1. The official gene symbol
2. The organism in which this gene is found.
Unfortunately, there is not a straightforward way to find official gene symbols in NCBI. The best practice is to go to the official genome database for your organism of interest. Here are databases for a few common organisms:
Let’s say that we found a really old paper that mentions the gene symbol GPR133 in humans. Let’s enter it into HGNC and see what happens.
This search returns 2 entries: ADGRD1 and it’s associated gene subfamily. Looks like the official symbol has changed. Let’s search for the official gene name in NCBI. The first step is finding the gene in the Gene Database. If you’re navigating from the main NCBI page, click on the dropdown menu to the left of the search box.
Then, we can search for this gene using its gene symbol with the [Gene Name] tag:
This search will return genes with that symbol from any organism:
Now you can pick the organism you’d like from the list. Next time i’ll explain how to find all the genes from a particular organism using the [Organism] tag, and go into some detail about the taxonomy database.
Thanks for reading
-Tobin Magle, Biomedical Sciences Research Support Specialist