Hi,
I have ensembl gene Ids from GRCh37.70 and I guess I need to use ensembl genes 70. But unfortunately, I can only find this linkin archive that leads to ensembl genes 75. I think I need ensembl gene 70.
Could anyone help me with this.
Thank you
2 answers
Yes, IDs should be (and mostly are) stable across releases if the gene model itself has not changed. However if there are changes in the gene model (even if there are 'minor' and does not affect the coding bits e.g. UTRs were extended), a new ENS ID will be assigned.
As we are comparing the models across different versions of the assembly, you may find gene A with ENS ID A in release 70, which got ENS ID B in release 86 (the structure of gene A could have changed). Check this previous post for more details.
Have you thought in getting GTF from the the Ensembl release 70 available in the Ensembl FTP?
Archive older than 3 years old (plus a few exceptions) are not maintained for browser access but are available through the FTP.
Do gene IDs change when UTRs change? Surely the extent of a UTRs etc, is a transcript thing?
Also, when does the revision number get increased rather than the whole ID changing
e.g. When is ENSGXXXXXXXXX.1 changed to ENSGXXXXXXXXX.2 and when is it changed to ENSGYYYYYYYYY?
IDs should be stable across releases I think. That is if an ID exists in both releases, it should refer to the same thing. Thus if your ID exists in the latest ensembl, then it will reffer to the same gene or transcript (although the structure of that gene or transcript may have changed). If the ID does not exist in Ensembl 86, then that gene/transcript (not just the ID) has been retired, and you won't be able to find a corresponding ID however good your conversion is.
Log in to answer this question.
-
biomaRt not finding all genes
written by danielcgingerich •
-
Different Ensembl Ids point to the same gene symbol.
written by elefth.pavlos •
-
BiomaRt: archive version of ensembl not working
written by salamandra
-
help with GDCprepare
written by lawarde.ankita1 •
-
ensembl transcript id to gene symbol using biomart
written by hxlei613
-
Ensembl API versions
written by SGW1 •
-
Discrepancy in gene counts between GENCODE 23 and Ensembl 81/82?
written by Veerendra Gadekar •
-
plant version of biomart
written by zizigolu
-
Extracting Data With Biomart / Problems
written by pcmubs •
-
Mapping Snps To Genes (And Pathways, Go, Etc.)
written by Stephen
Currently available archives are 67, 74 and 75 so you would need to use of one of those. This table shows the various assemblies present in those versions.