entrez id

[Zofia Wicik]

Dear sir/Madam

I cannot figure out how to get an annotation (UCSC or RefSeq) containing Entrez Gene Ids and eventually all known synonyms for a gene. I was able to find any other types of IDs but I cannot find a table containing the entrez numbers (Gene id). I'd be grateful for help with this issue.

best regards,

Zofia

[Jairo Navarro Gonzalez]

Hello Zofia,

Thank you for using the UCSC Genome Browser and your inquiry.

You can get the Entrez numbers by using the knownToLocusLink table and gene symbols using the kgXref table. For example, using the Data Integrator, you can use these tables to get both the Entrez IDs and other gene aliases by following these steps:

Step 1: Configure the Data Integrator

group: Mammal 
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
region to annotate: genome

Step 2: Configure Data Sources

For my example, I will be using the knownGene table, which corresponds to the UCSC annotation dataset.

track group: Genes and Gene Predictions
track: GENCODE v24 (knownGene)

After selecting this table, click Add.

Step 3: Configure Output Options

After adding the knownGene table, click Choose fields.
On the pop-up window, you can select all of the fields you are interested in from the knownGene table. 
From the Related tables section, add the hg38.kgXref and hg38.knownToLocusLink tables.

You can now select the Gene Symbol and RefSeq ID from the kgXref table 
and Entrez Gene ID from the knownToLocusLink table.

Once you have finished selecting your gene aliases, click get output. If you would like to have the output saved to a file, click the Send output to file checkbox.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute

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