gene names for ENSEMBL ID

[Bogdan Tanasa]

Dear all, please would you remind us how we can find the gene names for a set of ENSEMBL IDs ? ENSG00000000003.14

ENSG00000000005.5

ENSG00000000419.12

ENSG00000000457.13

ENSG00000000460.16

........

thanks a lot, 

-- bogdan

[Luis Nassar]

Hello Bogdan,

Thank you for using the UCSC Genome Browser and your question regarding converting Ensembl IDs to UCSC stable IDs. 

In case this explanation is not sufficient, I'd like to point you towards archived resources that may help further:

How to obtain the Ensembl transcript ID version number?

https://groups.google.com/a/soe.ucsc.edu/forum/#!msg/genome/nxRjQnsYcaE/MkSR1y-zJAAJ

get genes informations having ensemblID with mysql query

https://groups.google.com/a/soe.ucsc.edu/forum/#!msg/genome/ZIfPnw6jyUk/2c5u94QaOLgJ

You can accomplish this using the UCSC Table Browser. You can find it here:

http://genome.ucsc.edu/cgi-bin/hgTables

For your selections:

- Clade: Mammal

- Genome: Human

- Assembly: GRCh38 (or whichever you wish to use)

- Group: Genes and Gene Predictions

- Track: All Gencode V28

- Make sure 'Genome' is selected

- Identifiers: Hit the 'paste list' or the 'upload list' button and enter your Ensembl IDs

- Skip the next few lines until you get to 'output format' and select 'selected fields from primary...'

At this point you can choose a name in the 'output file' field if you wish to export results, or alternatively, you can leave it black and hit the 'get output' button to see them on your web browser.

- In the next page, check the box under 'Linked Tables', which is wgEncodeGencodeAttrsV28

- Then select the 'allow selection from checked tables' button

- From this new table check the geneID and geneName boxes

Finally hit the 'Get output' button and your results should be as follows:

ENSG00000000460.16 C1orf112

ENSG00000000460.16 C1orf112

ENSG00000000457.13 SCYL3

ENSG00000000457.13 SCYL3

ENSG00000000457.13 SCYL3

ENSG00000000460.16 C1orf112

ENSG00000000460.16 C1orf112

ENSG00000000460.16 C1orf112

ENSG00000000003.14 TSPAN6

ENSG00000000005.5 TNMD

ENSG00000000003.14 TSPAN6

ENSG00000000003.14 TSPAN6

ENSG00000000419.12 DPM1

ENSG00000000419.12 DPM1

(You'll need to do some mild tailoring in this case, you can look into the 'uniq' command on unix if you'll be working on command line)

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.

Lou Nassar

UCSC Genomics Institute

Training videos & resources: http://genome.ucsc.edu/training/index.html

Want to share the Browser with colleagues?

Host a workshop: http://bit.ly/ucscTraining

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[Bogdan Tanasa]

that is very helpful, thanks a lot Luis !