Hello everyone!
I'm currently on a project that requires the use of BrainEAC's data. Additionally, another component of the project requires a correspondence between the genes in BrainEAC and the genes available in other databases (with different assemblies).
To do this, we used the tool BioMart to be able to make the correspondence between BrainEAC's Ensembl transcript IDs (ENSTID) - for each one of the available total transcripts (tIDs) - and the Ensembl gene ID (ENSGID) in BioMart's data. With that, we found the overlapping ENSGIDs between BrainEAC and the other databases.
However, after doing this analysis we found two separate issues:
First issue found
When we were making the correspondence with the ENSGIDs, we found that some tIDs were matched with two or more ENSGIDs.
Let's take for example of a tID that corresponds to three different ENSTIDs in BrainEAC. After verifying the location of these ids we found that one of them is in chromosome 11 whereas the other two are in chromosome 1. As such, in the end, this tID was matched with different genes in different chromosomes.
Second issue found
Some ENSTIDs do not correspond to the positions of the tID they are part of in BrainEAC.
For example, we used a tID that showed three different ENSTIDs in BrainEAC and, then, we made the correspondence between those ENSTIDs and BioMarts data. With that, we found that two of them correspondend to one gene and the other one corresponded to another one.
This is concerning because one of the genes corresponded to another tID in BrainEAC's data with completely different positions in the genome. Furthermore, the position in the human assembly GRCh37 for the aforementioned gene is not inside the tID position interval in BrainEAC.
I would like to know if anyone has encountered these problems when using BrainEAC because it seems to be a problem with the data.
