Mapping metabolites against pathway databases
- 2. DATA ACQUISITION Separation Detection SAMPLING EXTRACTION DATA PROCESSING File Conversion Baseline Correction Peak Detection Deconvolution Adduct Annotation Alignment Gap Filling STATISTICS Normalization Multivariate Analysis (Parametric, Nonparametric) Univariate Analysis (Unsupervised, Supervised) BIOLOGICAL INTERPRETATION Pathway Mapping Network Enrichment STUDY DESIGN VALIDATION COMPOUND IDENTIFICATION Molecular Formula ID Structure ID MS Library Search Database Search In silico Fragmentation WCMC UC Davis
- 3. Question : Which metabolites from my list can be mapped to metabolic pathways ? Approach : Database mapping Results: A. Table of pathways with statistics B. Maps overlaid with detected metabolites C. Metabolites not mapped to pathways
- 4. Data preparation C00003 C00016 C00019 C00020 C00025 C00047 C00064 C00082 C00086 C00099 C00105 Select the KEGG database identifiers for compounds having pvalue <0.05 in your experiment. To get the KEGG ids for your compound list, you can use PubChem identifier exchange service. https://pubchem.ncbi.nlm.nih.gov/idexchange/idexchange.cgi
- 5. Prepare the compound list Sort the statistical results by p-value Select the KEGG ids of compounds with p-value <0.05 Use filter in Excel Example study : “spring_2018_metabolomics_course_pathway_example.xlsx” in the PathwayAnalysis_example folder
- 6. Four major databases for pathway mapping – • KEGG • Reactome • HMDB • Consensus path db For a comprehensive list of pathway databases – go to http://www.pathguide.org/
- 7. KEGG : Kyoto encyclopedia of genes and genomes http://www.genome.jp/kegg/ GO TO KEGG is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.
- 8. http://www.genome.jp/kegg/ Click on KEGG Mapper (at the bottom of the page)
- 9. Click on search pathway
- 10. Copy and paste the KEGG Ids in this box Click on execute Change organism if needed
- 11. KEGG Results - Click on the a pathway to get the map with compound overlaid on it.
- 12. KEGG Global metabolic map Red dots are the compounds present in the metabolite list.
- 13. Green boxes are enzymes mapped to the human genome. White boxes are enzymes not mapped to the human genome. Red circle shows the presence of this compound in the metabolite list
- 14. Reactome pathway mapping www.reactome.org “REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic and clinical research, genome analysis, modeling, systems biology and education. Founded in 2001, the Reactome project is led by Lincoln Stein of OICR, Peter D’Eustachio of NYULMC, Henning Hermjakob of EMBL-EBI, and Guanming Wu of OHSU.”
- 15. www.reactome.org
- 16. Copy and paste KEGG Ids in this box. # first line should be “#Small_molecules_KEGG”
- 19. Zooming in and double clicking will show the map of a pathway Metabolite in the list
- 20. MetaboAnalyst Pathway Mapping “To provide a user-friendly, web-based analytical pipeline for high-throughput metabolomics studies. In particular, MetaboAnalyst aims to offer a variety of commonly used procedures for metabolomic data processing, normalization, multivariate statistical analysis, as well as data annotation. The current implementation focuses on exploratory statistical analysis, functional interpretation, and advanced statistics for translational metabolomics studies.” http://www.metaboanalyst.ca/
- 21. Go to www.metaboanalyst.ca Click here
- 22. Paste the KEGG ids and select the type of identifiers Click : Submit Click : Submit Select a pathway library Click : Submit
- 23. Results Pathway topology : centrality of compounds
- 24. Output table Pathway with FDR < 0.20 are selected
- 25. Compound-pathway mapping is not provided
- 26. Consensus PathDB Metabolic Network Mapping “ConsensusPathDB-human integrates interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways. Data originate from currently 32 public resources for interactions (listed below) and interactions that we have curated from the literature. The interaction data are integrated in a complementary manner (avoiding redundancies), resulting in a seamless interaction network containing different types of interactions.” http://cpdb.molgen.mpg.de/
- 27. Click here http://cpdb.molgen.mpg.de/ Copy and paste KEGG id list here.
- 29. Results Click on select “all” Pathway similarity network
- 30. Pathway network
- 31. Click here http://cpdb.molgen.mpg.de/ Copy and paste KEGG id list here.
- 32. Input KEGG ids are mapped to internal ids and to various databases. Click on “all” to select them. Then click on the show interactions button.
- 33. CPDB Interaction Results Click on “all” to select them and then click on map and visualize interactions.
- 35. Discussions
- 36. Key points : • Not all detected metabolites have KEGG identifiers. • Not all compounds with KEGG ids can be mapped to metabolic pathways. • Pathway maps may not show all the reaction known for a metabolite. • Several compound appeared in many pathways. • Online tools can map metabolite list to pathway maps and perform pathway over-representation analysis for metabolites. • Online network visualization of a large number of metabolites is not efficient.
- 37. KEGG - 495 MetaCyc - 2453 Reactome - 2000 HMDB – 613 Wikipathways - 789 Note : Pathway definitions are manual and vary across different databases. Major pathway databases How many pathway we know so far ?
- 39. http://onlinelibrary.wiley.com/doi/10.1002/9781444339956.ch12/summary Caution! Can we trust a genome-derived pathway map ?
- 40. Glucose belongs to ? KEGG DB Reactome DB Pathway boundaries are arbitrary
- 41. Chemical-similarity maps of small molecules and metals in human blood Rappaport, Stephen M., et al. "The blood exposome and its role in discovering causes of disease." Environmental Health Perspectives (Online)122.8 (2014): 769. Node size = number of pathways Node size = Epidemiological studies • Epidemiologists and systems biologists / biochemist don’t study same compounds. • Epidemiologist seem to study compounds having a lesser number of known pathways. Do everyone care about pathways ?Do everyone care about pathways ?
- 42. Which TCA definitions ? KEGG Reactome SMPDB MetaCyc Which TCA definition ?
- 43. P <0.10 P <0.05 Which p-value : < 0.05 OR < 0.10 decide the p-value cutoff to get the list of input metabolites.
- 44. Metabolite pathway analysis: how about pathway topology ? Shall they have a same score ? Topology scoring If affected compounds are in close biochemical proximity, the pathway should be given a weightage score.
- 45. Fahrmann et al 2017 Gene Ontology TCA map -include gene names or symbols in the map Use pathway maps for focused biochemical visualization
- 46. Use pathway maps for focused biochemical visualization Pathway maps provided by databases are not used by publications. Authors draw their own maps and show data on it. https://www.nature.com/articles/cddis2011123
- 47. How to create these customized maps ? (Re) read biochemistry books and draw them OR
- 48. How to create these customized maps ? Metabolites Reactions Genes Pathway layout Biochemical databases Metabolomics dataset Cytsocape + powerpoint **No automated way exits to make pretty looking customized pathway maps. ProteinsKEGG HMDB MetaCyc Wikipathways Reactome Use biochemical databases
- 49. Next questions : • How to map all the identified metabolites into a biochemical network ? • How to show all the known reactions for a metabolite ? • How to map publishable network graphs ?
Editor's Notes
- #39: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-99