GTEX geneModel has more entries than gene
Kotlar, Alex
To whom it may concern,
It appears that there are fewer entries in the gtexGene than gtexGeneModel, on both hg38 and hg19. I’ve checked the distinct number of transcripts, and those are definitely different.
Could you help me understand why some gtexGeneModle transcripts are missing expression data? Is this a limitation of GTEX, or related to choices you made during import/data cleaning?
Thank you,
Alex
Alex Kotlar, PMP
PhD Candidate
Emory University Genetics & Molecular Biology
617-776-1459
ako...@emory.edu
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Jairo Navarro Gonzalez
Hello Alex,
Thank you for using the UCSC Genome Browser and your inquiry.
One of our engineers has investigated your issue and found that 925 gene entries were not included in the gtexGene track as they lacked GENCODE attribute annotation. Further investigation shows that GENCODE dropped these entries from its gene set. The gtexGene track relies on attributes from GENCODE, such as whether the gene is coding/non-coding/pseudo-gene.
Also, two different GENCODE versions were used to create these tracks. The gtexGene track used the GENCODE v24 annotations, the latest at the time, whereas the gtexGeneModel used the older GENCODE v19 annotations.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genomics Institute
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Kotlar, Alex
Thank you Jairo for your response,
Do you have any Gencode v24 expression data available? The gtexGene obviously lacks expression values.
Thank you,
Alex
Alex Kotlar, PMP
PhD Candidate
Emory University Genetics & Molecular Biology
617-776-1459
ako...@emory.edu
Jairo Navarro Gonzalez
Hello Alex,
Thank you for sending your follow-up question.
I wanted to clarify a message I sent in my previous response:
Also, two different GENCODE versions were used to create these tracks. The gtexGene track used the GENCODE v24 annotations, the latest at the time, whereas the gtexGeneModel used the older GENCODE v19 annotations.
The gtexGene and gtexGeneModel tracks, on hg19 and hg38, both were built using the GENCODE v19 annotations. However, 925 gene entries were not included in the gtexGene track as they lacked GENCODE v24 attribute annotation or were dropped in the newer GENCODE version 24. GENCODE v24 was the latest annotation release at the time of creating the GTEx Gene tracks.
We are doing some further investigation into your inquiry to see if we have expression data for any of these newer GENCODE releases.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genomics Institute
Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining
Jairo Navarro Gonzalez
Hello Alex,
Thank you again for using the UCSC Genome Browser. An engineer shares that we plan to update GTEx tracks later this year, after the final project data release (V8). If you would like email updates about the UCSC Genome Browser, please subscribe to our Announcements List:
- Subscribe: Email genome-annou...@soe.ucsc.edu
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I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genomics Institute
Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining
Kotlar, Alex
Thank you Jairo. Truly appreciate your dedication to the project.