In afukushima/MSEApdata: Metabolite-set data collection for pathway analysis in metabolomics

The MSEApdata package is the companion to MSEAp. It contains the following, which are necessary for metabolite-set enrichment analysis with MSEAp:

Metabolite-set data

MSEAp::supported.msets() lists all available metabolite-sets for MSEAp.

MSEAp::supported.msets()

Example data for MSEAp

We included mset_AraCyc_format_KEGG and mset_PlantCyc_format_KEGG, both for plant metabolomics study.

Example of metabolite-set expansion

As an example of metabolite-set expansion, we converted Reactome open-data to gmt file format (In our case, MSEA is performed instead of GSEA. So the gene IDs in the ordinary gmt file format are replaced by the metabolite IDs.) and imported the Reactome metabolite gmt files to rda data format in data directory. Please check data-raw/reactome2gmt.py and data-raw/gmt2rda.R in MSEApdata package to reproduce the process.

You can also import Wikipathways open-data to MSEAp with MSEAp::read.wikipathways(). But the metabolite IDs in Wikipathways open-data are not unified to KEGG or HMDB ID format. So you need some procedure to properly handle the IDs at some timing.

References

1. Caspi, R., et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2016;44(D1):D471-480.
2. Kanehisa, M., et al. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017;45(D1):D353-D361.
3. Fabregat, A., et al. The Reactome Pathway Knowledgebase. Nucleic Acids Res 2017.
4. Slenter, D.N., et al. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Res 2018;46(D1):D661-D667.

Session information {.unnumbered}

Here is the output of sessionInfo() on the system on which this document was compiled:

sessionInfo()

afukushima/MSEApdata documentation built on May 3, 2019, 11:52 p.m.