Question: Visualizing the position of many genes a time
0
gravatar for panagiotix
3.7 years ago by
panagiotix10
panagiotix10 wrote:

Hi all,

I have a family of genes (over 400 seperate genes) and I want to visualize their position on genome/chromosomes. That means, to get a map of chromosomes indicating the position of each of these genes. Is there any software/online tool to do so?

Thank you very much, Panos

genome gene • 1.8k views
ADD COMMENTlink modified 3.7 years ago by bernatgel2.6k • written 3.7 years ago by panagiotix10
6
gravatar for Alex Reynolds
3.7 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

If you can convert your data into GFF3-formatted elements, GenomeTools offers gt sketch that might help you out. Render into PDF and you can do markup with Adobe Illustrator or Inkscape.

You can also look into preparing a custom track on the UCSC Genome Browser.

Once you have added your custom track, you can use the Genome Graphs functionality to visualize it on chromosome ideographs (you can also visualize other signals with the same tool) and the View > PDF menu option to export a PDF file.

Browser shot

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Alex Reynolds30k

Thank a lot! That indeed helped me a lot.

ADD REPLYlink written 3.7 years ago by panagiotix10
4
gravatar for bernatgel
3.7 years ago by
bernatgel2.6k
Barcelona, Spain
bernatgel2.6k wrote:

If you can use R you can use karyoploteR for this.

If your genes are in a bed file you can plot them with

library(karyoploteR)
library(regioneR)

genes <- toGRanges("genes.file.bed")

kp <- plotKaryotype(genome="hg19")
kpPlotRegions(kp, data=genes)

and you will get something like this

genome plot with 400 gene positioned on it

You can add additional data, the gene names for example, or customize the appearance however you want. You can find more details at the karyoploteR tutorial page.

ADD COMMENTlink modified 11 months ago • written 3.7 years ago by bernatgel2.6k

Nice example — will put this in the bank!

ADD REPLYlink written 3.7 years ago by Alex Reynolds30k
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