Question: How To Visually Display What Protein Domains Are Affected By A Mutation
5
gravatar for Kasthuri
7.4 years ago by
Kasthuri270
United States
Kasthuri270 wrote:

Gurus,

I have a list of mutations and I want to see on which domains those mutations are (like kinase, C2, N-terminal, Helicase etc.). And I want them in nice plot like this:

Human TP53

DMDM (http://bioinf.umbc.edu/dmdm/) doesn't get me exactly what I need. I know how to get those domains as a text.

Any help?

Thanks -Kasthuri

protein • 8.1k views
ADD COMMENTlink modified 6.6 years ago by Aaronquinlan11k • written 7.4 years ago by Kasthuri270
1

Is this the same question as How To Create Mutation Diagram In R Or In Any Tools?? Is it the data or the plot you're struggling with?

ADD REPLYlink written 7.4 years ago by Ben2.0k

Yes...thanks! I don't want to plot them. I just want to make a quick inspection of the domain compared to the other domains in the gene of interest.

ADD REPLYlink written 7.4 years ago by Kasthuri270

what do you mean with "... of the domain compared to the other domains" ?

ADD REPLYlink written 7.4 years ago by Pierre Lindenbaum129k

I mean the mutations that occur in a particular domain compared with domains where the mutation is not present. Several hotspot mutations occur in, say, kinase domains compared to C2 and other areas of low complexity. Of course, it depends on the gene of interest...

ADD REPLYlink modified 7.4 years ago • written 7.4 years ago by Kasthuri270
6
gravatar for Aaronquinlan
6.6 years ago by
Aaronquinlan11k
United States
Aaronquinlan11k wrote:

I highly recommend the recently published GPViz software package. It is very simple to use and has all the customization features I have needed.

Download: http://icbi.at/software/gpviz/gpviz.shtml

Manuscript: http://bioinformatics.oxfordjournals.org/content/early/2013/06/19/bioinformatics.btt354.full.pdf

Drop in a gene model file in GTF format, a variant file in VCF format, and a domain model file (human models from Ensembl are available on the GPViz download page) and you are good to go.

Example

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Aaronquinlan11k
3
gravatar for henryvuong
7.4 years ago by
henryvuong780
USA
henryvuong780 wrote:

If all you need is the domain information, you can search pfam website, for example (http://pfam.sanger.ac.uk/protein/P53_HUMAN). Then, you can map your list of mutation to the domain start and end. For the plot, I found this website from cBio helpful : https://code.google.com/p/cbio-cancer-genomics-portal/wiki/RFC_5_Mutation_Diagrams. Also, I wrote an R script that can give similar plot using grid package (still need to refine). Hope it helps.

ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by henryvuong780
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