Hi, 

I have a list of transcripts, such as: ENST00000416191. I want to find the Ensembl IDs for the genes they are associated with. Would I get identical results, whether I query GRCh38 or GRCh37? Note that I am not interested in their coordinates, only the IDs.

Thank you
Hi jiab,
to  give you an idea of the differences here is a little bash script, which gives you a list of ENSTs mapping to different ENSGs in grch37 and grch38:

    #!/bin/bash
    #download of all ENST mapped to ENSG from Ensembls grch37 biomart
    wget -O mapping_37.txt 'http://grch37.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query  virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "1" count = "" datasetConfigVersion = "0.6" ><Dataset name = "hsapiens_gene_ensembl" interface = "default" ><Attribute name = "ensembl_transcript_id" /><Attribute name = "ensembl_gene_id" /></Dataset></Query>'

    #download of all ENST mapped to ENSG from Ensembls grch38 biomart
    wget -O mapping_38.txt 'http://www.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE Query> <Query  virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "1" count = "" datasetConfigVersion = "0.6" >  <Dataset name = "hsapiens_gene_ensembl" interface = "default" > <Attribute name = "ensembl_transcript_id" /> <Attribute name = "ensembl_gene_id" /> </Dataset> </Query>'

    #join the two mappings on ENST
    join <(sort mapping_37.txt) <(sort mapping_38.txt) >joined_on_ENST.txt

    #get just the lines, where ENSGs differ for grch37 and grch38 for the same ENST
    awk '$2!=$3 {print $1, $2, $3}' joined_on_ENST.txt >different_ENSG_37_38.txt

If you have a look at the number of lines in each file: 

      wc -l *
     1421 different_ENSG_37_38.txt
     190566 joined_on_ENST.txt
     215170 mapping_37.txt
     218207 mapping_38.txt
It shows you that the mappings in 37 and 38 share about 190k ENST having 25k (37) and  28k (38) unique ENSTs and 1421 ENSTs mapping to different ENSG in both builds.
Out of about 243k different ENSTs (190566 +25k+28k) you could search your ENSG for, in the different versions, you would not get the same result for both builds (no ENSG in one build, or different ENSG) for about 54k queries (25k+28k+1421).
