Finding regulatory or structural elements

Question

[blur]

Hi,

I have peaks that are expected to fall into areas outside genes, that might or might not have structural elements or a specific regulatory area.

The people doing the bench work don't know what to expect.

The question is - is there a smart way to check for such elements? A list of peaks will not be very informative... Are there databases that list all regulatory/structural elements I can intersect my data with? I found this but am not sure if it considered good enough: http://www.ensembl.org/info/genome/funcgen/regulatory_features.html

Thanks!

Answer 1

[Papyrus]

In R, you can use the AnnotationHub package to access lots of datasets hosted at the AnnotationHub. It is useful because you can easily explore the database within R, and also because datasets are provided as R data classes and are easily accessed (see vignette). For example, as of today it lists over 15000 Ensembl datasets:

library(AnnotationHub)
ah <- AnnotationHub()

The metadata can be directly explored as a data.frame:

metadata <- mcols(ah)

Or queried with the query function which works like a kind of grep

ens <- query(ah,"Ensembl")
ens

AnnotationHub with 15126 records
# snapshotDate(): 2019-10-29 
# $dataprovider: Ensembl, UCSC, BioMart, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Pan troglodytes, Bos taurus, Gallus gallus, Tetraodon nigroviridis, Sus scrofa, Felis ...
# $rdataclass: TwoBitFile, GRanges, EnsDb, data.frame, OrgDb, list
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, rdatapath,
#   sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH5046"]]'

(Also, for easy annotation of your peaks with custom annotations, I find the annotatr package to be intuitive).