Re: Assistance with obtaining gene names for archived ENS IDs at the UCSC Genome Browser
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Mohammad Goodarzi
Jan 23, 2018, 3:46:10 PM1/23/18
to Cath Tyner, gen...@soe.ucsc.edu
Hello,
I have a set of gene ensemble ID and I try to map them to gene name, I have mapped all data bases and some are missing while some are changed.
can you please help me to overcome this problem?
Please find the data in attachment
Thanks
Mohammad
On Tue, Jan 23, 2018 at 11:13 AM, Cath Tyner <ca...@ucsc.edu> wrote:
Hello Mohammad,I saw your request on the Ensembl dev forum - I work in User Support for the UCSC Genome Browser. You may want to see if our support team can provide a solution for you.If you are interested in this, please email the UCSC Genome Browser support team public help forum with a detailed request:Please also include about 10 of your ENS IDs so that we can use them in example output for you.>> Hello,>> Thank you for your reply.> Is it possible to guide me how to use one of your archive with Biomart or any other programming language ?> When it comes to 3000 genes , it is very difficult to do them one by one .>> Thanks> MohammadCathCath Tyner
. . .UCSC Genome Browser, Software QA & User SupportUC Santa Cruz Genomics Institute
Cath Tyner
Jan 23, 2018, 6:36:33 PM1/23/18
to Mohammad Goodarzi, UCSC Genome Browser Public Help Forum
Hello Mohammad,
Thanks for contacting the UCSC Genome Browser support team.
I took a quick look at your file with 60,488 rows, and it seems that most ENS IDs have at least some columns with gene names. If the suggestions below aren't sufficient to accomplish your goal, please reply to this forum with about 10 or so IDs that you are trying to match gene names to. In other words, please send a sample of only the ENS IDs that you are having problems with, and let us know exactly the goal you wish to accomplish, with examples. This way, we can use your example ENS IDs to help you.
Below are some related previously answered mailing list questions that may help, and please also feel free to search our forum archive for related posts: https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome
Getting the ENS version number from Ensembl's Biomart tool:
Mapping UCSC IDs to ENS IDs
Mapping old-to-new UCSC IDs
Getting old gene IDs from hg19
Using MySQL to query for ENS IDs:
Using the Table Browser tool to get gene symbols
As you move forward, please feel free to respond to this forum at any time if our support team can provide further assistance, and please always feel free to search our mailing list archives for related posts.
Thank you for contacting the UCSC Genome Browser support team.
Please send new and follow-up questions to one of our mailing lists below:
* Confidential/private help: Email
genom...@soe.ucsc.eduMohammad Goodarzi
Jan 23, 2018, 7:30:04 PM1/23/18
to Cath Tyner, UCSC Genome Browser Public Help Forum
Hello,
can you please annotate these genes
| ensembl_gene_id |
| ENSGR0000002586 |
| ENSGR0000124333 |
| ENSGR0000124334 |
| ENSGR0000167393 |
| ENSGR0000168939 |
| ENSGR0000169084 |
| ENSGR0000169093 |
| ENSGR0000169100 |
| ENSGR0000178605 |
| ENSGR0000182162 |
| ENSGR0000182378 |
| ENSGR0000182484 |
| ENSGR0000185203 |
| ENSGR0000185291 |
| ENSGR0000185960 |
| ENSGR0000196433 |
| ENSGR0000197976 |
| ENSGR0000198223 |
| ENSGR0000205755 |
| ENSGR0000214717 |
| ENSGR0000223274 |
| ENSGR0000223484 |
| ENSGR0000223511 |
| ENSGR0000223571 |
| ENSGR0000223773 |
| ENSGR0000225661 |
| ENSGR0000226179 |
| ENSGR0000227159 |
| ENSGR0000228410 |
| ENSGR0000228572 |
| ENSGR0000229232 |
| ENSGR0000230542 |
| ENSGR0000234622 |
| ENSGR0000234958 |
| ENSGR0000236017 |
| ENSGR0000236871 |
| ENSGR0000237040 |
| ENSGR0000237531 |
| ENSGR0000237801 |
| ENSGR0000263835 |
| ENSGR0000263980 |
| ENSGR0000264510 |
| ENSGR0000264819 |
| ENSGR0000265658 |
| ENSGR0000270726 |
| ENSGR0000275287 |
| ENSGR0000276543 |
| ENSGR0000277120 |
| ENSGR0000280767 |
| ENSGR0000281849 |
Thanks
Mohammad
Cath Tyner
Jan 23, 2018, 9:31:11 PM1/23/18
to Mohammad Goodarzi, UCSC Genome Browser Public Help Forum
Hello again Mohammad,
Thank you for the refined list of example IDs! I'm assuming these are in regard to human genes? If they are for a different organism, please respond to this forum and let us know.
I've found the following GENCODE resource which I believe may apply to your example cases:
Why do some gene and transcript ids start with ENSGR or ENSTR in the GTF/GFF3?Since the GTF convention dictates that feature ids have to be unique for different genome regions, we slightly modify the Ensembl feature id by >replacing the first zero with an "R". Thus, "ENSG00000182378.10" in chromosome X becomes "ENSGR0000182378.10" in chromosome Y.
If we convert your list to replace the "R" with a "0", e.g.,
sed 's/R/0/g' yourENSGRexamples.txtENSG00000002586ENSG00000124333ENSG00000124334
...and then use the converted list, I can find matches of these ENSG IDs both in the UCSC Genome Browser as well as Ensembl.
There are ways to obtain gene names and other annotations for these ENSG ids in the UCSC Genome Browser, but if you just want gene names, it's probably most efficient to just use Ensembl's BioMart tool.
Doing so, I got 45 (out of your 50) results:
Gene stable ID Gene nameENSG00000002586 CD99ENSG00000124333 VAMP7ENSG00000124334 IL9RENSG00000167393 PPP2R3BENSG00000168939 SPRY3ENSG00000169084 DHRSXENSG00000169093 ASMTLENSG00000169100 SLC25A6ENSG00000178605 GTPBP6ENSG00000182162 P2RY8ENSG00000182378 PLCXD1ENSG00000182484 WASH6PENSG00000185203 WASIR1ENSG00000185291 IL3RAENSG00000185960 SHOXENSG00000196433 ASMTENSG00000197976 AKAP17AENSG00000198223 CSF2RAENSG00000205755 CRLF2ENSG00000214717 ZBED1ENSG00000223274 RNA5SP498ENSG00000223484 TRPC6PENSG00000223511 AL683807.1ENSG00000223571 DHRSX-IT1ENSG00000223773 CD99P1ENSG00000225661 RPL14P5ENSG00000226179 LINC00685ENSG00000227159 DDX11L16ENSG00000228410 ELOCP24ENSG00000228572 AL954722.1ENSG00000229232 KRT18P53ENSG00000230542 LINC00102ENSG00000234622 AL683807.2ENSG00000234958 FABP5P13ENSG00000236017 ASMTL-AS1ENSG00000236871 LINC00106ENSG00000237040 DPH3P2ENSG00000237531 AL672277.1ENSG00000237801 AMD1P2ENSG00000265658 MIR3690ENSG00000270726 AJ271736.1ENSG00000275287 Metazoa_SRPENSG00000277120 MIR6089ENSG00000280767 AL732314.4ENSG00000281849 AL732314.6
At this point, you may want to double check with Ensembl just to make sure we're on the right track here, but if your list is derived from a GTF/GFF file, then this may be the direction to move forward with. If this is the case, then it looks like you may already have at least some of these ENSGids in your Genenames.xlsx file already.
As you move forward, please feel free to respond to this forum at any time if our support team can provide further assistance, and please always feel free to search our mailing list archives for related posts.
Thank you for contacting the UCSC Genome Browser support team.
Please send new and follow-up questions to one of our mailing lists below:
* Confidential/private help: Email
genom...@soe.ucsc.eduEnjoy,
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