What are the important features for pathway analysis?

MetaboAnalystis offers a free, web-based tool for pathway analysis based on targeted metabolomics data.

  • Algorithm: it integrates many well-established (i.e. univariate analysis, over-representation analysis ) methods, as well as novel algorithms / concepts (GlobalTest, GlobalAncova, pathway topology analysis) into pathway analysis.
  • Pathway database: pathways are defined based on KEGG metabolic pathways (~25 organisms) and [SMPDB](https://www.smpdb.ca/) (human/mouse)
  • Visualization: implements a Google-Map style interactive visualization system to help users understand their analysis results. These simplified pathways are hyperlinked to their original pathways in KEGG and SMPDB

MetaboAnalyst also supports pathway analysis for LC-MS based untargeted metabolomics data based on mummichog in its Functional Analysis module.

For targeted metabolomics data, there are many commercial pathway analysis software tools, such as Pathway Studio, MetaCore, Ingenuity Pathway Analysis, etc .