How To Visualize Gene Fusions To Better Illustrate The Gene Structure?
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9.5 years ago
kendric.wang ▴ 150

I would like to visualize gene fusions in a way that illustrates the gene structure (primarily exons) of belonging to the normal gene partners and how they are joined to form the fusion (similar to the figure below). For a few events, I could draw this manually, but I'd like to create figures for hundreds of fusion events. Are there free or commercial tools available for this? I know people have typically visualized fusion events in IGV or using circos plots (e.g. FusionAnalyser), but this is not exactly what I'm looking for. Thanks.

Example of gene fusion!

fusion • 11k views
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To answer my own question, here are two promising tools for visualizing gene structure:

FancyGene (http://bio.ieo.eu/fancygene/)

  • generating the image requires uploading a formatted file into interface, so it's not ideal for automatic high-throughput generation of figures

FeatureStack (http://bioinformatics.oxfordjournals.org/content/28/23/3137.full)

  • can automate generation of figures
  • visualizations not as refined compared to first software
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I'm interested in handy visualization tools, and I'm eager to see what ends up working for your. But I also wanted to comment so I can find this later. It's another example of a nice little project for some student to generate with real-world value.

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Hi,

I am also interested in visualizing fusion genes the way you depicted in your example for TMPRSS2-ERG.

Please share your solution, if you have found one.

Thanks!

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5
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9.5 years ago
terdon ▴ 430

I'm not sure how it deals with fusions but gff2ps is a great tool for this kind of visualization. It was used to produce the images and printable posters for the Celera Human Genome assembly. It is, admittedly, not very easy to use but incredibly powerful. Having spent a few years working next to its author I can also assure you that he is very nice and very open to questions so you should be able to contact him if you need help.

For some examples of what gff2ps is capable of see here.

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neat tool, I just realized that I got so used to bitmap graphics that it was refreshing to see output that one can actually zoom in

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It really is a great tool once you manage to get it to work. The documentation is really hard though. When I used to work with him, we would always just ask the author to sort it out for us :). On the bright side, it is open source and written in Perl so it is editable.

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I'll give this a try. Thanks!

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6.9 years ago
stianlagstad ★ 1.1k

I've compiled a list of programs, tools, and strategies to visualize gene fusions/genomic rearrangements here: Which program, tool, or strategy do you use to visualize genomic rearrangements?

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