I try to fetch gene symbols from coordinate ranges (in good old hg19 space). It works perfectly except for one region where I get FIP1L1 in first position before the expected PDGFRA while the two genes are not even overlapping. Actually, FIP1L1 is located quite far downstream from PDGFRA.
Could someone explain this behavior and how to avoid it?
You can reproduce my result with:
library("biomaRt") ensembl=useMart(host='feb2014.archive.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL', dataset="hsapiens_gene_ensembl") getBM(attributes = "hgnc_symbol", filters = c('chromosome_name','start','end'), values = list("4","55127193","55127663"), mart=ensembl)
# 1 FIP1L1
# 2 PDGFRA
This is true for several intervals as seen in IGV
UCSC confirms the 'fraud' (disclaimer, this was a joke and I apology if I did hurt people's feeling)