Lecture 25

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Pathways and Networks

A general reference for this section is the book chapter

Intermolecular Interactions and Biological Pathways

Gary D. Bader, Anton J. Enright

in Bioinformatics 3E Eds. Andreas D. Baxevanis and B.F.Francis Ouellette. John Wiley and Sons, New Jersey

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Ref: Pathway information for systems biology
Cary MP, Bader GD, Sander C, FEBS Lett. 2005 Mar 21;579(8):1815-20
Available from http://baderlab.org/Publications

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Text book versions of pathways are often not cell specific - they lack context in time and space because experimental method generally don’t have the power to map pathways at this level of resolution or we are not organized enough as a community to map one pathway in one cell. Genomic and proteomic approaches will help us map whole pathways with single experimental methods in individual cell types in the future.

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Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Ho Y et al. Nature 2002 Jan 10;415(6868): 180-183
Available from http://baderlab.org/Publications

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Active modules reference:
Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 2002;18 Suppl 1:S233-40.
http://www.pathblast.org/
http://www.agilent.com/labs/research/mtl/projects/sysbio/sysinformatics/litsearch.html

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Movie can be downloaded from http://www.studiodaily.com/main/searchlist/6850.html
or download from http://baderlab.org/Home?action=AttachFile&do=get&target=InnerCellLife.mov