Question

Create Chromosome Wide Distribution Map

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12.8 years ago

Nitin ▴ 170

Hi all,

I have 185 genes (gene symbols) and corresponding affymetrix ids..I want to create chromosome wide distribution map ..Using R/Bioconductor..or any other tool..

Can anybody let me know how to do it?

Thanks in advance

Nitin

r bioconductor chromosome mapping • 4.6k views

ADD COMMENT • link updated 12.8 years ago by Eric Fournier ★ 1.4k • written 12.8 years ago by Nitin ▴ 170

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More details required. What exactly is a chromosome wide distribution map? You just want to plot their chromosomal locations?

ADD REPLY • link 12.8 years ago by Neilfws 49k

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yes i want map all 185 genes on to chromosome map which would show where particular gene is located on chromosome.

ADD REPLY • link 12.8 years ago by Nitin ▴ 170

score 2 · Answer 1 · 2012-02-01

2

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12.8 years ago

Sean Davis 27k

Take a look at the ggbio, ideogram, and geneplotter Bioconductor packages. For a non-bioconductor approach, have a look at Circos.

ADD COMMENT • link 12.8 years ago by Sean Davis 27k

score 2 · Answer 2 · 2012-02-01

You can try the UCSC's hgGenome tool to generate chromosomal mappings for certain model organisms.

In your case, assuming you are working on the human genome:

Use the Tables tool to create a custom track based on UCSC Genes, but filtered to only contain your specific gene IDs
Import your custom track in the hgGenome tool.