[BioC] How to plot microRNA chromosome location

[Camper (Chih-Wei Liu)]

That helps. Thank you very much.

-camper

==================================================
Camper Chih-Wei Liu
National Cheng Kung University, Tainan, Taiwan
Department of Computer Science and Information Engineering
Intelligent Information Retrieval Lab: IIR Lab 
camper at cad.csie.ncku.edu.tw


-----Original Message-----
From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com] 
Sent: Tuesday, October 28, 2008 9:14 AM
To: Camper (Chih-Wei Liu)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] How to plot microRNA chromosome location

Hi,

On Oct 27, 2008, at 6:39 PM, Camper (Chih-Wei Liu) wrote:

> Hi all,
>
>
>
> I have check some useful packages to plot gene chromosome  
> information like
> gene plotter, ideogram and GenomeGraphs.
>
> However, I don't know how to plot microRNA (miRNA) chromosome  
> location.
>
> I would like to see the distribution of some miRNAs in the genome.
>
>
>
> I have known the miRNA chromosome info.
>
> miRNA name           chromosome           start           end
>
> hsa-miR-130b            22                             20337592      
> 20337673
>
> hsa-miR-33a              22                             40626894
> 40626962
>
> hsa-miR-15b              3                              161605069
> 161605166
>
> .
>
>
>
> Is there any packages that I provide the location and plotting it out?

You could create a custom track and upload it to the UCSC genome  
browser.

It looks like you got your info about 90% the way to GFF format:

http://genome.ucsc.edu/FAQ/FAQformat#format3

You could tweak your info a bit, then write.table your way to a file  
you can upload as a UCSC custom track.

Is that good enough, or were you looking for something more? And if  
so, what? There's the GenomeGraphs library, which is pretty slick, but  
I'm not sure if that's really what you're after:

http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html

Hope that helps,

-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Cornell Medical College of Cornell University

http://cbio.mskcc.org/~lianos