This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Genomic position to genomic feature

Hi, We have some Methylation samples and obtained some differentially methylated regions (DMR) from those samples. Now we are asking are those DMR makes biological sense. So we want to know if a DMR is in promoter, gene body, intron, exon, repeat regions, or low complexity regions. To test the promoter and gene body we have collected a database and checked whether a DMR falls in the gene body or promoter. But the problem is with intron, exon, repeat regions, or low complexity regions. Is there any database for those features where for a given genomic position (e.g. chr10:100006425), we can know where (intron, exon, repeat regions, or low complexity regions) it falls?

genome dmr methylation
• 1,625 views • link
written by irfanwustl • irfanwustl

For genes (exons, introns, promoters, UTRs...) if you are using R and working on human or a fairly common model organism, you can use Bioconductor's TxDb objects. For example TxDb.Hsapiens.UCSC.hg38.knownGene for human or TxDb.Mmusculus.UCSC.mm10.knownGene/ for mouse.

You can find some documentation in their respective vignettes or here for a more general view, but you'd basically be using genes, exons, ... functions.

• 0 views • link
written by bernatgel bernatgel

0 answers

No answers yet.

Log in to answer this question.

More posts like this