Metabolic Network Mapping Exericse
- 1. Unit 5.2 Metabolic network visualization (exercise) Dinesh Barupal dinkumar@ucdavis.edu
- 2. Input file : MetaMapp R- Package (openCPU version) Network file Node attribute file How to use MetaMapp ?
- 3. How to use MetaMapp ? Prepare the input file. Example : TeachingMaterialDataSetsBioinformatics_Training_DataMetaMappNull_MetaMapp_input.xlsx
- 4. MetaMapp input file errors - • Duplicate PubChem CIDs • Duplicate names • Missing SMILES codes • Missing p-value or fold-change • Headers mismatch • > 1000 compounds
- 5. How to use MetaMapp ? Obtaining the MetaMapp files. • Go to http://metamapp.fiehnlab.ucdavis.edu Copy and paste your data in this box Click here Now, click on these two buttons chemsim_krp_07.sif node_attributes_chemsim_krp_07.tsv Both files are provided in the training data folder for the case study.
- 6. chemsim_krp_07.sif node_attributes_chemsim_krp_07.tsv Structure of the created files. Both files will be imported in the Cytoscape software for visualization KRP – KEGG Reaction Pairs – biochemical relationships TMSIM – Tanimoto similarity – chemical relationships
- 7. What is Cytoscape ? The most used network visualization and analysis tool. http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.1001843http://www.cytoscape.org/ Backed by strong institutions
- 8. Visualize a range of experimental data on a network graph Useful graph layout algorithms Graph theory calculations Easy organization of multiple networks for comparisons. Faster navigation of large networks Filter and query the network Contributed plugins Works on PC, Max and Linux system USB drive contains a copy of Cytoscape software Cytoscape basic features
- 9. Start Cytoscape software Locate the chemsim_krp_07.sif file and click import. The file shall be in your download folder or you can use the file in the example folder. How to use Cytoscape?
- 10. Visualization panel Table panel highlights the data related to selected node (yellow). Cytoscape windows
- 11. Useful buttons in the menu-bar Zoom in Zoom out Zoom-all Zoom in selected You will use these often.
- 12. Show graphics details Tip: if you don’t see the labels/edges/shapes/colors in graph, click on “Show graphics details”.
- 13. Visualize using the yFiles (organic layout). You can try other layout methods, but this one is recommended. Layout a network graph
- 14. Now import your Node Attributes file
- 15. Import your Node Attributes file
- 16. Import your Node Attributes file “Key” symbol should be PubChem_ID
- 17. Import your Node Attributes file Table panel after importing the node attributes.
- 18. Data visualization All visual properties can be accessed in the style tab. Node color Node size Node label Node label position Node Label font size Edge color Edge width Network background color Left bottom corner
- 19. Change network background color 1 2 3 Select black background color or any color you like.
- 20. Switch back to the node visual properties Click on the node tab.
- 21. Double click here click here Node coloring : “Node Fill color”
- 22. Red = higher in male mouse Blue = higher in female mouse Yellow = no change Node coloring : “Node Fill color”
- 23. Change node label You can choose any label from the node attribute file. You need to zoom in to see the labels Use the scroll button to zoom in and out.
- 24. If you don’t see the labels
- 25. Intermediate network graph crowded, overlapping labels and unpublishable.
- 26. Change label font size Showing labels for only the significant compounds. It is bit clearer.
- 27. Change node size Select the values by press the left click on mouse. Then right click. Node size rules FC 1.0 – size = 20 FC >1 & <2 --size = 60 FC >2 & < 3 -- size = 100 FC >3 & < 5 --size = 150 FC > 5-- size = 200
- 28. Visualize using the yFiles (organic layout). You can try other layout methods, but this one is recommended. Apply the organic layout Not yet publication ready
- 29. Node moving Press “control” key and click left mouse button and select the area Now you can move these nodes
- 30. Change edge colors This box must be checked. The visual property is under the subtab – “edge”
- 31. Intermediate network graph Lipids Amino acids and amines sugars nucle Not yet publication ready
- 32. Cluster detection Check this box Large network can be divided into smaller modules for better visualization and interpretation
- 34. Clustered network Phospholipids TG, DG, MG, FA CEs Nucleotides Aromatics Peptides Sphingolipids Amino acids
- 35. Create a sub-network Select a cluster by pressing “Ctrl” and then left click and make a square box. Once selected the nodes, Prese Ctrl+N to make a new network Show graphics details
- 36. Node label position Click on the label position It will make label position property available in the style tab.
- 37. Select right side nodes Click on this box to change the property for selected node. Drag the object box to the left and click ok Node label position
- 38. Select left side nodes Click on this box to change the property for selected node. Drag the object box to the left and click ok Node label position
- 39. Increase the scaling factor to remove the overlaps of labels. Scaling Focused view of the phospholipid cluster.
- 40. Network navigation Click on a network you want to visualize Create subnetworks for – • Sphingolipids • Cholesteroyl esters • TGs • Phopspholipids • One carbon metabolism
- 41. Phospholipids cluster Cholestroyl esters Sphingolipids and amino acids Focused visualization of clusters Clearer, readable, less crowded. This can go in a paper.
- 42. Save the session for future
- 43. Export the network as a pdf file