tutorial- building biochemical and chemical similarity networks
DESCRIPTION
A brief tutorial and link to R functions to get you started building biochemical and chemical similarity networks using R and Cytoscape.TRANSCRIPT
Building Biochemical + Chemical Similarity Networks
Dmitry Grapov, PhD040413
The ingredients
1. List of chemical identifiers
• Preferably - Pubchem compound identifiers (CIDs)
2. Edge List (calculate from identifiers or database)
3. Table of Edge/Node Attributes (calculate from data or database)
4. Visualization
Some Examples
Biochemical relationships + chemical similarity + correlation + statistics + PLS-DA
Biochemical relationships + chemical similarity + correlation + statistics + PLS-DA + graphs
partial correlation + PLS-DA + statistics + graphs
correlation + class information + clustering + PLS-DA + MDS
correlation + clustering + OSC-PLS-DA + Statistics
The ingredients
1. List of chemical identifiers
• Preferably - Pubchem compound identifiers (CIDs)
2. Edge List (calculate from identifiers or database)
3. Table of Edge/Node Attributes (calculate from data or database)
4. Visualization
Edge List
1. KEGG RPAIRS
2. Tanimoto distances
3. Other options
• correlations
• partial-correlations
• similarity/dissimilarity measures
4. (optional) edge attributes
Node Attributes Table
Options for node mapping
1. Continuous: size, transparency, boarder width, color
2. Discreet: color, shape, label
3. Other: node graphics
Demonstration
1. Get nessesary R code2. chemical identifiers 3. Import into R 4. Create KEGG RPAIRs edge list5. Create Tanimoto similarity edge list 6. Node attributes table
Visualizing network in Cytoscape
1) Up load edge list(save as excel file first)
Visualizing network in Cytoscape
1) Up load edge list
Visualizing network in Cytoscape
Change layout
Visualizing network in Cytoscape2) Up load node attributes file
Visualizing network in Cytoscape2) Up load node attributes file
Visualizing network in Cytoscape3) Map node and edge attributes
Visualizing network in Cytoscape
4)When done export network to favorite file format