MGV: a generic graph viewer for comparative omics data
| Autor: | Stephan Symons, Kay Nieselt |
|---|---|
| Rok vydání: | 2011 |
| Předmět: |
Proteomics
Statistics and Probability Visual analytics Computer science Systems biology computer.software_genre Models Biological Biochemistry Transcriptome Software Metabolomics Computer Graphics Cluster Analysis Cluster analysis Molecular Biology business.industry Gene Expression Profiling Systems Biology Graph Layout Pathway analysis Omics Graph Computer Science Applications Visualization Computational Mathematics Computational Theory and Mathematics Data mining business computer Data integration |
| Zdroj: | Bioinformatics. 27:2248-2255 |
| ISSN: | 1367-4811 1367-4803 |
| DOI: | 10.1093/bioinformatics/btr351 |
| Popis: | Motivation: High-throughput transcriptomics, proteomics and metabolomics methods have revolutionized our knowledge of biological systems. To gain knowledge from comparative omics studies, strong data integration and visualization features are required. Knowledge gained from these studies is often available in the form of graphs, and their visualization is especially useful in a wide range of systems biology topics, including pathway analysis, interaction networks or gene models. Especially, it is necessary to compare biological models with measured data. This allows the identification of new models and new insights into existing ones. Results: We present MGV, a versatile generic graph viewer for multiomics data. MGV is integrated into Mayday (Battke et al., 2010). It extends Mayday's visual analytics capabilities by integrating a wide range of biological models, high-throughput data and meta information to display enriched graphs that combine data and models. A wide range of tools is available for visualization of nodes, data-aware graph layout as well as automatic and manual aggregation and refinement of the data. We show the usefulness of MGV applied to several problems, including differential expression of alternative transcripts, transcription factor interaction, cross-study clustering comparison and integration of transcriptomics and metabolomics data for pathway analysis. Availability: MGV is a open-source software implemented in Java and freely available as a part of Mayday at www.microarray-analysis.org/mayday. Contact: symons@informatik.uni-tuebingen.de Supplementary information: Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
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