Question: Converting full Protein names into Gene ID
0
gravatar for pbio
5.3 years ago by
pbio140
United States
pbio140 wrote:

HI all,

I have a list which contains certain list of Protein names and it looks like this, these are full names with respect to each protein. Now the problem is to find out the gene names from the list of full protein names.

CYP3A1
CYSTATIN C
CYTOCHROME P450
CYTOCHROME P450 11B2, MITOCHONDRIAL
CYTOKERATIN 16
CYTOKERATIN 18
CYTOKERATIN 18 M30/M65 RATIO
CYTOKERATIN 19
D-DIMER

I know tools like DAVID and Biomart, which can do the conversion for short protein names to gene ids. Is there a way to convert this list to geneIDS?

protein gene • 2.8k views
ADD COMMENTlink modified 5.3 years ago by Jean-Karim Heriche24k • written 5.3 years ago by pbio140

Are these all you have, or are there a lot more names in your list.  Generally you would need an official identifier to use conversion tools.  Are there any other columns in your file that may contain these?

ADD REPLYlink written 5.3 years ago by alolex910
2
gravatar for Jean-Karim Heriche
5.3 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche24k wrote:

These look like gene names to me (in the sense of the HGNC's full gene name). You could use the Ensembl API to match them to all gene names and synonyms in the database. Hopefully this would get you a fair number. The problem is these names are often ambiguous and have sometimes been assigned to different genes. This is why it's better to rely on database identifiers (with the proper database version).

ADD COMMENTlink written 5.3 years ago by Jean-Karim Heriche24k
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