Introduction

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 biological 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.

Publications

  1. AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.
    Cite this
    Emig D, Salomonis N, Baumbach J, Lengauer T, Conklin BR, Albrecht M, 2010-07-01 - Nucleic acids research
  2. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation.
    Cite this
    Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico AR, Cline MS, Clark TA, Williams A, Blume JE, Samal E, Mercola M, Merrill BJ, Conklin BR, 2010-06-01 - Proceedings of the National Academy of Sciences of the United States of America

Credits

  1. Dorothea Emig
    Developer

    Max Planck Institute for Informatics, 66123 Saarbrücken

  2. Nathan Salomonis
    Developer

  3. Jan Baumbach
    Developer

  4. Thomas Lengauer
    Developer

  5. Bruce R Conklin
    Developer

  6. Mario Albrecht
    Investigator

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Summary
AccessionBT000388
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByMario Albrecht