Building Biochemical + Chemical Similarity Networks

Dmitry Grapov, PhD 040413

The ingredients
1. 2. List of chemical identifiers Preferably - Pubchem compound identifiers (CIDs) Edge List (calculate from identifiers or database)

3.
4.

Table of Edge/Node Attributes (calculate from data or database)

Visualization

Biochemical relationships + chemical similarity + correlation + statistics + PLS-DA

Some Examples

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. 2. List of chemical identifiers Preferably - Pubchem compound identifiers (CIDs) Edge List (calculate from identifiers or database)

3.
4.

Table of Edge/Node Attributes (calculate from data or database)

Visualization

Edge List
1. 2. 3. KEGG RPAIRS Tanimoto distances 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. 2. 3. 4. 5. 6. Get nessesary R code chemical identifiers Import into R Create KEGG RPAIRs edge list Create Tanimoto similarity edge list 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 Cytoscape 2) Up load node attributes file

Visualizing network in Cytoscape 2) Up load node attributes file

Visualizing network in Cytoscape 3) Map node and edge attributes

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