8 network mapping II

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From a series of lectures for the 2014 WCMC LC-MS Data Processing and Statistics for Metabolomics short-course (http://metabolomics.ucdavis.edu/courses-and-seminars/courses).

Download all the material:
http://sourceforge.net/projects/teachingdemos/files/Winter%202014%20LC-MS%20and%20Statistics%20Course/Winter%202014%20LC-MS%20and%20Statistics%20Course.zip/download

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8 network mapping II

  1. 1. Biology Chemistry Informatics Biochemical and Structural Similarity Network Mapping Network Mapping Goal: Generate a mapped biochemical product/substrate and chemical similarity network Topics: 1. Edge list generation 2. Node attributes generation 3. Network Mapping
  2. 2. Biology Chemistry Informatics Biochemical and Structural Similarity Network Mapping Network Mapping Steps 1. Use MetaMapR to generate: url: https://github.com/dgrapov/MetaMapR • Biochemical and structural similarity based edge list for all metabolites with KEGG and PubChem identifiers. • Network preview • Node attributes 1. Use previously generated Pumpkin/Tomatillo analysis results to generate node attribute mappings 2. Visualize and map network using Cytoscape
  3. 3. MetaMapR: Edge List Biology Chemistry Informatics Network Mapping Download the generated edge list, overview and save as an .xlsx file (for ease of import).
  4. 4. Preview Network Biology Chemistry Network Mapping Informatics
  5. 5. Node Attributes Biology Chemistry Network Mapping Informatics
  6. 6. Biology Chemistry Network Mapping Informatics Mapping Analysis results to Node Attributes Labels: Shape: Direction of metabolite Index change relative to matching names pumpkin edge list Color: Direction of change Border: O/PLS/-DA ID for significantly changed selected feature? species (t-Test) Size(a): log of the magnitude of fold change Size(b): O/PLS/-DA LV 1 loadings
  7. 7. Mapping in cytoscape Biology Chemistry Network Mapping Informatics
  8. 8. Biology Chemistry Informatics Biochemical and Spectral Similarity Mapped Network for: Differences in Pumpkin and Tomatillo Leaf Primary Metabolites Network Mapping Leaf fatty acids are decreased and phytosterols increased in tomatillo compared to pumpkin Tomatillo displays a general increases in leaf carbohydrates with the exception of raffinose and trehalose, which are importantly decreased in tomatillo compared to pumpkin Helps withstand prolonged periods of desiccation intermediate for lignin synthesis, related to quinic acid which is an astringent A trisaccharide, can not be digested by humans, but readily fermented by bacteria
  9. 9. Summary Biology Chemistry Network Mapping Informatics View all files and mappings used in the network construction in the: 1. Data folder • Pumpkin and Tomatillo data for network.csv 2. Network folder • Biochemical edge list.xlsx • Biochemical node attributes.xlsx • Biochemical network.cys (final network)

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