How can I find the location of a gene based on cytogenetic bands (e.g. 7q31.2)?
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@arman-shahrisa-7713
Last seen 2.7 years ago

How can I find the location of a gene based on cytogenetic bands (e.g. 7q31.2)? Is there any package(s) that lets me convert the gene symbol to cytogenetic bands?

bioconductor cytogenetics • 539 views
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@martin-morgan-1513
Last seen 22 days ago
United States

Organism.dplyr provides another fun option, exposing the org and TxDb databases as dplyr objects

> library(Organism.dplyr)
> src = src_ucsc("Human")
using org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene
> src
src:  sqlite 3.19.3 [/home/mtmorgan/.cache/BiocFileCache/5b377bf41425_5b377bf41425]
tbls: id, id_accession, id_go, id_go_all, id_omim_pm, id_protein,
  id_transcript, ranges_cds, ranges_exon, ranges_gene, ranges_tx
> tbl(src, "id") %>% filter(symbol %like% "BRCA%") %>% dplyr::select(map, symbol) %>% distinct()
# Source:   lazy query [?? x 2]
# Database: sqlite 3.19.3
#   [/home/mtmorgan/.cache/BiocFileCache/5b377bf41425_5b377bf41425]
       map  symbol
     <chr>   <chr>
1     5p12 BRCAT54
2 17q21.31 BRCA1P1
3    13q21   BRCA3
4 17q21.31   BRCA1
5  13q13.1   BRCA2
6    11q23  BRCATA

 

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I forgot about the MAP column. You can get this directly without having to engage with any of that tidyverse nonsense <shakes cane at kids on lawn>.

> select(Homo.sapiens, "BRCA2", "MAP", "SYMBOL")
'select()' returned 1:1 mapping between keys and columns
  SYMBOL     MAP
1  BRCA2 13q13.1
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@james-w-macdonald-5106
Last seen 1 hour ago
United States

The biovizBase package has a GRanges of the hg19 cytogenetic bands, so you could use that. There is also a GRanges with gene symbols in that package which makes it super convenient. Let's say we want the cytoband for BRCA2:

> library(biovizBase)
> data(hg19IdeogramCyto)
> data(genesymbol)
> subsetByOverlaps(hg19IdeogramCyto, genesymbol["BRCA2",])
GRanges object with 1 range and 2 metadata columns:
      seqnames               ranges strand |     name gieStain
         <Rle>            <IRanges>  <Rle> | <factor> <factor>
  [1]    chr13 [32200000, 34000000]      * |    q13.1   gpos50
  -------
  seqinfo: 24 sequences from an unspecified genome; no seqlengths

So BRCA2 is in 13q13.1. Is that what you are after?

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Exactly! Thank you very much.

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