What’s the Answer? (domain and lollipop mutation diagrams)

Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.

This week’s highlighted question is one that was initially raised a while back, but had new answers recently added so it floated back up to the top. And one of the new answers is a very nifty web-based quick solution that our readers often find particularly handy–I’ll mention it specifically below.

Question: How To Create Mutation Diagram In R Or In Any Tools?

Please let me know any tools or R packages that can create a mutation diagram showing mutations in protein domains like this figure from the MSKCC cBio Cancer Genomic Portal? Thanks in advance



There was some chatter about doing some DIY stuff, and some possible R packages that can get there, as well as existing ways to see these at some resource providers. But the new solution that was just added by Jeffk for a web-based easy to use implementation at the cBioPortal is what I wanted to focus on. Their “Mutation Mapper” interface will do the trick, with just a little bit of organizing your data in the right columns. There isn’t a lot of documentation with it, it was just recently released according to the notes. It seems limited to human genes. For other species you can try the other options in the answers. It would be great to see this made more widely available for other species as well.

PS: Other simple web interfaces for domains that we’ve talked about before that remain popular include DomainDraw and MyDomains. You could accomplish diagrams with some of the features with those as well.

Gao J., U. Dogrusoz, G. Dresdner, B. Gross, S. O. Sumer, Y. Sun, A. Jacobsen, R. Sinha, E. Larsson & E. Cerami & (2013). Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal, Science Signaling, 6 (269) pl1-pl1. DOI: http://dx.doi.org/10.1126/scisignal.2004088