Question: ENSEMBL Gene ID to Gene Symbol
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gravatar for Eliran Turgeman
6 weeks ago by
Eliran Turgeman10 wrote:

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?

gene • 311 views
ADD COMMENTlink modified 6 weeks ago by Jean-Karim Heriche23k • written 6 weeks ago by Eliran Turgeman10

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.

ADD REPLYlink written 6 weeks ago by Jean-Karim Heriche23k

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?

ADD REPLYlink written 6 weeks ago by Eliran Turgeman10
2

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.

ADD REPLYlink written 6 weeks ago by Jean-Karim Heriche23k
1

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? ).

ADD REPLYlink written 6 weeks ago by genomax89k

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)

ADD REPLYlink written 6 weeks ago by Eliran Turgeman10

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.

ADD REPLYlink written 6 weeks ago by genomax89k

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

ADD REPLYlink written 6 weeks ago by Eliran Turgeman10
1

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

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by genomax89k
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gravatar for Kevin Blighe
6 weeks ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

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

Another approach via mysql and UCSC:

Kevin

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Kevin Blighe65k
1
gravatar for devarora
6 weeks ago by
devarora230
SouthKorea
devarora230 wrote:

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.

ADD COMMENTlink written 6 weeks ago by devarora230
1
gravatar for Jean-Karim Heriche
6 weeks ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche23k wrote:

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.

ADD COMMENTlink written 6 weeks ago by Jean-Karim Heriche23k
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