The Centre for Applied Genomics (TCAG) and the Ontario Genomics Institute (OGI) hosted two 3-hour sessions on bioinformatics tools for
"Pathway and Network Analysis". The workshops were led by Dr. Gary Bader,
Dr. Quaid Morris
and Dr. Sylva Donaldson from the University of Toronto.
The sessions were aimed at all levels from graduate students to principal investigators, with the goal of benefiting both new and experienced researchers in the area of pathway and network analysis.
Presentations and computer labs/demos included:
• An overview of pathway analysis using Cytoscape by Dr. Gary Bader, including a hands-on demo of Cytoscape, an open source bioinformatics software for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other data sets
Click here to download the pathway and data analysis slides (given by Dr Gary Bader).
• An introduction to GeneMANIA by Dr. Quaid Morris, an algorithm for predicting gene function and gene interactions based on functional genomics data, including hands-on demo of the software prototype
Click here to download the gene function analysis slides (given by Dr Quaid Morris).
Additional information and articles related to the software demonstrated:
Click here to download a protocol for Biomart (as demonstrated during the session)
Click here to download a protocol for GeneMANIA (as demonstrated during the session)
Rhee et al. (2008) Use and misuse of the gene ontology annotations. Nat Rev Genet 9(7):509-515. (PMID: 18475267)
Yeung et al. (2008) Exploring biological networks with Cytoscape software. Curr Protoc Bioinformatics Sep; Chapter 8; Unit 8.13. (PMID: 18819078)
Cline et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2(10):2366-82. (PMID: 17947979)
Mostafavi et al. (2008) GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol. 9; Suppl 1: S4. (PMID: 18613948)
