[Bioc-devel] Cytogenetic bands

[Valerie Obenchain]

Hi Ilari,

org.Hs.eg.db is one of the packages included in Homo.sapiens and it's 
the origin of 'MAP'. This variable maps between entrez gene ids and 
cytoband names, not genomic coordinates (as you've discovered). It 
includes bands and sub-bands provided by Entrez Gene downloaded from here:

   ftp://ftp.ncbi.nlm.nih.gov/gene/DATA

To see a full description of 'MAP':

   library(org.Hs.eg.db)
   ?org.Hs.egMAP

We don't have an annotation package with cytoband coordinates but you 
can download them using rtracklayer:

library(rtracklayer)
session <- browserSession()
genome(session) <- "hg19"
query <- ucscTableQuery(session, "cytoBandIdeo")
tbl <- getTable(query)

>> dim(tbl)
> [1] 931   5

>> head(tbl)
>   chrom chromStart chromEnd   name gieStain
> 1  chr1          0  2300000 p36.33     gneg
> 2  chr1    2300000  5400000 p36.32   gpos25
> 3  chr1    5400000  7200000 p36.31     gneg
> 4  chr1    7200000  9200000 p36.23   gpos25
> 5  chr1    9200000 12700000 p36.22     gneg
> 6  chr1   12700000 16200000 p36.21   gpos50

Valerie


On 03/22/2014 10:12 AM, Ilari Scheinin wrote:
> Hi,
>
> I would like to obtain the boundaries of cytogenetic bands for human (hg19) as I need to map arbitrary genomic positions to the band containing them. I figured these would be available via the Homo.sapiens annotation package, so I took a look at the available keytypes. MAP looked promising:
>
>> library(Homo.sapiens)
>> head(keys(Homo.sapiens, keytype="MAP"))
> [1] "19q13.4"  "12p13.31" "8p22"     "14q32.1"  "3q25.1"   “2q35”
>
> However, upon a closer look, these don’t appear to be the actual bands themselves, but are instead the matching bands for some other level of data, as it contains entries such as "19q13-qter”. (And there are 2,446 of these entries whereas there are 862 bands.)
>
> A bit of searching returned two software packages that do contain this information: idiogram (data(Hs.cytoband)) and OmicCircos (data(UCSC.hg19.chr)). The first one seems to be from genome build hg17, but the second one has hg18 and hg19. However, using a software package instead of an annotation one to obtain this information seems wrong, and makes me worry if it will be kept up-to-date in the future (c.f. idiogram).
>
> So, are the coordinates of the cytogenetic bands contained somewhere in the annotation packages?
>
> Thanks,
> Ilari
>
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-- 
Valerie Obenchain
Program in Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B155
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: vobencha at fhcrc.org
Phone:  (206) 667-3158
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