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Building Biochemical + Chemical Similarity Networks

Building Biochemical + Chemical Similarity Networks. Dmitry Grapov, PhD 040413. List of chemical identifiers Preferably - Pubchem compound identifiers (CIDs) Edge List (calculate from identifiers or database) Table of Edge/Node Attributes (calculate from data or database) Visualization.

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Building Biochemical + Chemical Similarity Networks

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  1. Building Biochemical + Chemical Similarity Networks Dmitry Grapov, PhD 040413

  2. List of chemical identifiers • Preferably - Pubchem compound identifiers (CIDs) • Edge List (calculate from identifiers or database) • Table of Edge/Node Attributes (calculate from data or database) • Visualization The ingredients

  3. Biochemical relationships + chemical similarity + correlation + statistics + PLS-DA Some Examples

  4. Biochemical relationships + chemical similarity + correlation + statistics + PLS-DA + graphs

  5. partial correlation + PLS-DA + statistics + graphs

  6. correlation + class information + clustering + PLS-DA + MDS

  7. correlation + clustering + OSC-PLS-DA + Statistics

  8. List of chemical identifiers • Preferably - Pubchem compound identifiers (CIDs) • Edge List (calculate from identifiers or database) • Table of Edge/Node Attributes (calculate from data or database) • Visualization The ingredients

  9. KEGG RPAIRS • Tanimoto distances • Other options • correlations • partial-correlations • similarity/dissimilarity measures • (optional) edge attributes Edge List

  10. Options for node mapping • Continuous: size, transparency, boarder width, color • Discreet: color, shape, label • Other: node graphics Node Attributes Table

  11. Get nessesary R code • chemical identifiers • Import into R • Create KEGG RPAIRs edge list • Create Tanimoto similarity edge list • Node attributes table Demonstration

  12. Visualizing network in Cytoscape • 1) Up load edge list • (save as excel file first)

  13. 1) Up load edge list Visualizing network in Cytoscape

  14. Change layout Visualizing network in Cytoscape

  15. 2) Up load node attributes file Visualizing network in Cytoscape

  16. 2) Up load node attributes file Visualizing network in Cytoscape

  17. 3) Map node and edge attributes Visualizing network in Cytoscape

  18. 4)When done export network to favorite file format Visualizing network in Cytoscape

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