List of all promoter position

Question

[irfanwustl]

Is there a list of all promoters' genomic positions with gene names? From the UCSC table browser, I can get the annotation. But instead of gene id, this gives transcript_id. Any suggestion, please?

Answer 1

[rpolicastro]

Here's an R solution to get all transcript promoters with the corresponding gene name. This takes advantage of AnnotationHub, which is a repository and associated library that allows access to the annotation data for many organisms. I'll be using S. cerevisiae as an example here.

library("AnnotationHub")

ah <- AnnotationHub()
anno <- query(ah, c("cerevisiae", "txdb", "sacCer3"))[[1]]

promoters <- trim(promoters(anno, upstream=500, downstream=500, columns=c("tx_name", "gene_id")))

> head(promoters)
GRanges object with 6 ranges and 2 metadata columns:
            seqnames      ranges strand |     tx_name         gene_id
               <Rle>   <IRanges>  <Rle> | <character> <CharacterList>
    YAL069W     chrI       1-834      + |     YAL069W         YAL069W
  YAL068W-A     chrI     38-1037      + |   YAL068W-A         YAL069W
  YAL067W-A     chrI   1980-2979      + |   YAL067W-A       YAL067W-A
    YAL066W     chrI  9591-10590      + |     YAL066W         YAL066W
  YAL064W-B     chrI 11546-12545      + |   YAL064W-B       YAL064W-B
    YAL064W     chrI 21066-22065      + |     YAL064W         YAL064W
  -------
  seqinfo: 17 sequences (1 circular) from sacCer3 genome

You can export this as a bed file using rtracklayer::export if you want, or convert it to a data.frame with as.data.frame and save as a table with write.table.

Annotation files are usually held as TxDb objects in R. Any TxDb object will work with this, such as those from AnnotationHub like we used above, or explicit TxDb libraries like this example from yeast, or from a GTF fle using GenomicFeatures::makeTxDbFromGFF.