Hello,

after my first question (Gviz - Split a GeneRegionTrack by strand), I keep experimenting with Gviz but I have trouble understanding some behavior of BiomartGeneRegionTrack constructor.

When trying to use the 'symbol' argument to limit the result of annotation fetching from biomart, I observe a 'discrepancy' when using different genomes.

> annoTrack <- BiomartGeneRegionTrack(genome="hg18", name="ENSEMBL", symbol="ACTB");
> annoTrack
GeneRegionTrack 'ENSEMBL'
| genome: hg18
| active chromosome: chr7
| annotation features: 8
> min(annoTrack)
[1] 5533313
> max(annoTrack)
[1] 5536758

But when trying the same selection on "hg19" genome version, I get a huge range of genomic coordinates, and all associated annotations :

> annoTrack <- BiomartGeneRegionTrack(genome="hg19", name="ENSEMBL", symbol="ACTB");
> annoTrack
GeneRegionTrack 'ENSEMBL'
| genome: hg19
| active chromosome: chr7
| annotation features: 3176
> min(annoTrack)
[1] 70972
> max(annoTrack)
[1] 5603415

I think this is why I had trouble with my first post.

Can someone help me with this problem ?

Thank you.

My R version :
system         x86_64, linux-gnu                                 
status         Under development (unstable)                      
major          3                                                 
minor          3.0                                               
year           2015                                              
month          10                                                
day            14                                                
svn rev        69514

I believe the problem is link to data available via biomart in version hg19 there is additional gene with the same gene symbol.

http://grch37.ensembl.org/biomart/martview/d96a971d42e19b989d617c68a2109be3?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl.default.feature_page.ensembl_transcript_id|hsapiens_gene_ensembl.default.feature_page.start_position|hsapiens_gene_ensembl.default.feature_page.end_position|hsapiens_gene_ensembl.default.feature_page.hgnc_symbol|hsapiens_gene_ensembl.default.feature_page.chromosome_name&FILTERS=hsapiens_gene_ensembl.default.filters.hgnc_symbol."ACTB"&VISIBLEPANEL=resultspanel

which does not exist in previous version

http://may2009.archive.ensembl.org/biomart/martview/91586135767a99e1153709f1afa2d64a/91586135767a99e1153709f1afa2d64a/91586135767a99e1153709f1afa2d64a?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl.default.feature_page.ensembl_transcript_id|hsapiens_gene_ensembl.default.feature_page.chromosome_name|hsapiens_gene_ensembl.default.feature_page.start_position|hsapiens_gene_ensembl.default.feature_page.end_position|hsapiens_gene_ensembl.default.feature_page.hgnc_symbol&FILTERS=hsapiens_gene_ensembl.default.filters.hgnc_symbol."ACTB"&VISIBLEPANEL=resultspanel

hopefully this helps

Thank you !

I finally understand what happen.

However, should it be considered as a normal behavior ? These genes are not even defined on the same chromosome which explains why I could not find them in the GeneRegionTrack object nor in the plot.

I should have looked at the original database, a big thank you again for that !