How to Analyze KEGG Pathways of Differential Metabolites?
To analyze the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways of differential metabolites, the following steps can be followed:
Data Collection
First, it is essential to collect and prepare data on differentially expressed genes or metabolites. These data are typically obtained from transcriptomic or metabolomic experiments.
Data Preprocessing
The collected data must undergo necessary preprocessing, such as normalization and the selection of differentially significant metabolites or genes.
KEGG Pathway Mapping
Using the KEGG database, differentially expressed metabolites or genes are mapped to specific metabolic pathways. This can be achieved using online tools available on the KEGG website or various bioinformatics software packages, such as KEGGREST, KEGGgraph, etc.
Pathway Enrichment Analysis
Perform pathway enrichment analysis to identify which pathways are significantly enriched in your dataset. This can be done using software tools like DAVID, GSEA, MetaboAnalyst, and others.
Result Interpretation and Visualization
Based on the analysis results, interpret which pathways are affected and visualize these pathways. This can be accomplished using software packages such as Pathview, Cytoscape, etc.
Further Analysis
Depending on the requirements, additional analyses may be necessary, such as pathway dynamic simulations or flux balance analysis.
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