AltAnalyze and DomainGraph: analyzing and visualizing exon expression data
By D. Emig, N. Salomonis, Jan Baumbach, Thomas Lengauer, Bruce R. Conklin, Mario Albrecht. Nucleic Acids Res., 2010
326 citations recorded by the source corpus.
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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/df6597eb60f5219bc52fab6da263578526c51ef1
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In Molecular Biology
- Martina Kutmon
- Alexander R. Pico
- Chris T. A. Evelo
- M. V. Iersel
- Kristina Hanspers
- Thomas Kelder
- Bruce R. Conklin
- Carlos Martínez-A
Citations in the corpus
- WikiPathways: building research communities on biological pathways (2011, methodology): “An example of a locally installed tool that integrates WikiPathways content via the web service is DomainGraph (19), a plugin for the network analysis tool Cytoscape that can be used to visualize alternative-splicing data.”
- Topological analysis and interactive visualization of biological networks and protein structures (2012, methodology): “For instance, plug-ins such as ClusterMaker 49 , GLay 50 , MCODE 51 , MINE 52 and NeMo 53 can be used to identify and visualize clusters in networks, whereas the DomainGraph plug-in has a special focus on the visual analysis of the effect of alternative splicing on gene and protein networks 54 .”
- Dido3-dependent SFPQ recruitment maintains efficiency in mammalian alternative splicing (2019, methodology): “Initial classification of splicing alterations was performed by Altanalyze software (44).”