ENSEMBL Gene ID to Gene Symbol

Question

[Eliran Turgeman]

I came across this site which offers some tools for converting ENSEMBL gene id to gene symbol. I wanted to inquire about what are the conversion set of rules?

[Jean-Karim Heriche]

What do you mean by set of rules? We've gone off into giving lists of tools but maybe this is not what you're asking.

[Eliran Turgeman]

Is there a one to one conversion between ENSEMBL gene id to gene symbol? Is it just a huge table or there are some rules that given an ENSEMBL I can convert it to gene symbol?

[Jean-Karim Heriche]

You have to understand that Ensembl IDs and gene symbols represent different notions of what a gene is. In Ensembl, a gene is a portion of a chromosome. A gene symbol on the other hand is an attempt at summarizing and standardizing many names given to a "gene" by biologists. The definition of gene used by biologists is fuzzy and usually refers to a set of related molecules (e.g. proteins or RNAs) that may be produced by more than one locus in the genome.

[GenoMax]

ID's are logically mapped based on annotations and other experimental information. There need not be a 1:1 correspondence in these ID's (A: How to deal with the case that one gene symbol matches multiple ensembl ids? ).

[Eliran Turgeman]

So assuming I have this ENSEMBL : ENSMUSG00000022485 can I deduce from the numbers what is the gene symbol? without using a database? The bottom line is that I want to write a script that handels such conversion (two sided)

[GenoMax]

Your best bet is to use the API posted by @Jean-Karim below. Other solutions will need you to install/use R code or query MySQL.

[Eliran Turgeman]

Could you elaborate on how can I query from MySQL? where can I find the relevant databases?

[GenoMax]

@Kevin linked that answer below. Check: A: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates You are going to query the public databases.

Answer 1

[Kevin Blighe]

Please take a look at the first two answers here for the 2 most common programmatic approaches:

• Conversion of Gene Name to Ensembl ID

Another approach via mysql and UCSC:

• A: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates

Kevin

Answer 2

[tothepoint]

Either you can use the biomaRt R package or just use Ensembl BioMart to convert Ensembl-id to gene name in BioMart and choose a specific database and fetch your query.

Answer 3

[Jean-Karim Heriche]

There's also the perl API to Ensembl. No need to do raw SQL queries against the database and it's much more convenient when one needs to access and process different types of entities/information.