AltAnalyze and DomainGraph: Analyzing and visualizing exon expression data

Dorothea Emig, Nathan Salomonis, Jan Baumbach, Thomas Lengauer, Bruce R. Conklin, Mario Albrecht

Research output: Contribution to journalArticlepeer-review

236 Scopus citations

Abstract

Alternative splicing is an important mechanism for increasing protein diversity. However, its functional effects are largely unknown. Here, we present our new software workflow composed of the open-source application AltAnalyze and the Cytoscape plugin DomainGraph. Both programs provide an intuitive and comprehensive end-to-end solution for the analysis and visualization of alternative splicing data from Affymetrix Exon and Gene Arrays at the level of proteins, domains, microRNA binding sites, molecular interactions and pathways. Our software tools include easy-to-use graphical user interfaces, rigorous statistical methods (FIRMA, MiDAS and DABG filtering) and do not require prior knowledge of exon array analysis or programming. They provide new methods for automatic interpretation and visualization of the effects of alternative exon inclusion on protein domain composition and microRNA binding sites. These data can be visualized together with affected pathways and gene or protein interaction networks, allowing a straightforward identification of potential biologic-al effects due to alternative splicing at different levels of granularity. Our programs are available at http://www.altanalyze.org and http://www. domaingraph.de. These websites also include extensive documentation, tutorials and sample data.

Original languageEnglish
Article numbergkq405
Pages (from-to)W755-W762
JournalNucleic Acids Research
Volume38
Issue numberSUPPL. 2
DOIs
StatePublished - 29 May 2010
Externally publishedYes

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