Question: How to find CpG island for specific region
0
gravatar for mootthedoot2
5.4 years ago by
Croatia
mootthedoot20 wrote:

How can you get the descritption of CpG island for a specific region of a specific chromosome in the UCSC genome browser? It should contain the GC ratio and content, length and so on.

I would like only this range chrX:22,823,930-33,137,478. I tried and couldnt find how to do that.

Thanks a lot in advance!
 

 

I always get send here:

http://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chrX%3A24339661-34653209&hgsid=200067334_unRimKm5TVcsljUPrkZnlFEAXOvc

genome • 4.4k views
ADD COMMENTlink modified 5.4 years ago by PoGibas4.8k • written 5.4 years ago by mootthedoot20

There are more than 20 CpG islands in the given region (>10Mb). Do you need statistics for all of them?

ADD REPLYlink written 5.4 years ago by PoGibas4.8k
3
gravatar for PoGibas
5.4 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

Simple solution:

  1. Go to UCSC browser -> Select "Tools" -> Select "Table Browser".
  2. Enter "genome/assembly" you're interested in.
  3. Enter "region" (coordinates for your CpG islands) and mark "position".
  4. Select "group" - "Regulation" and "track" - "CpG islands".
  5. Click "get output".

# Sample output
#bin chrom chromStart chromEnd name length cpgNum gcNum perCpg perGc obsExp
763 chrX 23350284 23350596 CpG: 25 312 25 195 16 62.5 0.83
763 chrX 23351142 23353639 CpG: 197 2497 197 1448 15.8 58 0.94
765 chrX 23685406 23686046 CpG: 66 640 66 425 20.6 66.4 0.96


You can find explanation about columns ("cpgNum", "perGc") under the "describe table schema" in "Tools/Table Browser".

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by PoGibas4.8k

Thanks a lot!

ADD REPLYlink written 5.4 years ago by mootthedoot20
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