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Metabolic pathway visualization

Martijn van Iersel & Chris Evelo BiGCaT Bioinformatics Maastricht University. Metabolic pathway visualization. PathVisio. http://www.pathvisio.org. Van Iersel et al., BMC Bioinformatics. 2008 Sep 25;9(1):399. http://www.pathvisio.org.

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Metabolic pathway visualization

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  1. Martijn van Iersel & Chris Evelo BiGCaT Bioinformatics Maastricht University Metabolic pathway visualization

  2. PathVisio http://www.pathvisio.org Van Iersel et al., BMC Bioinformatics. 2008 Sep 25;9(1):399.

  3. http://www.pathvisio.org Van Iersel et al., BMC Bioinformatics. 2008 Sep 25;9(1):399.

  4. WikiPathways http://www.wikipathways.org Pico et al., PLOS Biology 6 (7):e184

  5. 1. (+)-Lactate 2. (+)-Lactic acid 3. (S)-(+)-2-Hydroxypropanoate 4. (S)-(+)-2-Hydroxypropanoic acid 5. (S)-2-Hydroxypropanoic acid 6. (S)-2-Hydroxypropionate 7. (S)-2-Hydroxypropionic acid 8. (S)-2-hydroxy-Propanoate 9. (S)-2-hydroxy-Propanoic acid 10. (S)-Lactate 11. (S)-Lactic acid 12. (alpha)-Lactate 13. (alpha)-Lactic acid 14. 1-Hydroxyethane 1-carboxylate 15. 1-Hydroxyethane 1-carboxylic acid 16. 1-Hydroxyethanecarboxylate 17. 1-Hydroxyethanecarboxylic acid 18. 2-Hydroxypropanoate 19. 2-Hydroxypropionate 20. L-2-Hydroxypropanoate 21. L-2-Hydroxypropanoic acid 22. Milk acid 23. Sarcolactic acid 24. a-Hydroxypropanoate 25. a-Hydroxypropionate 26. a-Hydroxypropionic acid 27. alpha-Hydroxypropanoate 28. alpha-Hydroxypropionate 29. l-(+)- lactic acid 30. alpha-Hydroxypropionic acid Identification

  6. (s)-lactate [lactate] adenosine diphosphate (adp) "n,n-dimethylglycine“ nad+ citrate/isocitrate lys his leu d-fucose Helpful clarification Superfluous quote symbol Ambiguous identifications Polypeptides Non-human metabolites Problematic names

  7. Identification • CAS 50-99-7 • + Largest database, – Not public • HMDB HMDB00122 • * Biology-oriented, * Focus on human, - Relatively small • ChEBI CHEBI:17634 • * Chemistry-oriented, * Ontology approach PubChem • Compound: 5793 • Substance: 833240 Kegg Compound C00031 Chemspider 5589

  8. Identification Hierarchical ontology of compounds - ChEBI

  9. Lactate CHEBI:24996 Lactic acid CHEBI:28358 Don’t know / don’t care HMDB00190

  10. Future: Use of compartments

  11. Future: SBGN

  12. Multi-omics visualization • Dynamic visualization of simulations • BioPAX import / export • MSEA

  13. http://www.pathvisio.orghttp://www.wikipathways.org Gladstone Insitutes (San Francisco, USA) Alexander Pico Kristina Hanspers Bruce Conklin Department of Bioinformatics (Maastricht, NL) Martijn van Iersel Thomas Kelder Chris Evelo TNO Food & Nutrition (Zeist, NL) Suzan Wopereis Jildau Bouwman Ben van Ommen

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