How Can KEGG Analysis Results Be Visualized?
When performing analyses using KEGG (Kyoto Encyclopedia of Genes and Genomes), a variety of tools and approaches are available for effective visualization of the results:
KEGG Mapper
KEGG Mapper is a web-based tool that enables the visualization of KEGG annotations, such as genes, metabolites, or other biological entities, within the context of KEGG pathway diagrams. Users can input data such as gene expression levels or metabolite concentrations and select appropriate analysis modes, including enrichment analysis or gene set comparison. The tool then generates pathway maps with annotated elements highlighted based on the input data.
KEGG API
KEGG provides a set of application programming interfaces (APIs) that allow programmatic access to KEGG data. Through the KEGG API, annotation results can be retrieved and downloaded for local use, enabling customized analysis and visualization using specialized tools. For example, Python libraries such as 'matplotlib' or R packages like 'ggplot2' can be employed to generate graphical representations of KEGG annotation outcomes.
Cytoscape
Cytoscape is a robust platform for network analysis and visualization that facilitates the representation of interactions among genes, proteins, and metabolites within KEGG pathways. KEGG annotation data can be loaded into Cytoscape, where users have the flexibility to apply a variety of layout algorithms and visualization schemes to explore and interpret the underlying biological networks.
R Packages and Tools
The R programming environment offers a rich ecosystem of packages tailored for KEGG-based analysis and visualization. For instance, the 'KEGGREST' package facilitates access to KEGG databases; 'KEGGgraph' allows for the construction and visualization of KEGG pathway graphs; and 'pathview' integrates KEGG annotations with gene expression or other omics data for pathway-based visualization. These tools collectively support detailed, customizable visual interpretation of KEGG results within the R framework.
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