Lecture 23

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Computational analysis of pathways and interaction networks

 

BCH441 Guest lecture:

Gary Bader

Terrence Donnelly Center for Cellular and Biomolecular Research (DCCBR)

BBDMR, MedGen, DCS, SLRI

University of Toronto

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

 

Links summary

• Bader Lab - publications
  
• Kurt Kohn's signalling maps at the NIH
  
• Sea urchin development gene regulatory pathways
  
• Pathguide: the pahway resource list
  
• The Cancer Cell Map
  
• Pathway Commons
  
• Cytoscape - biological graph visualization and analysis
  
• MCODE - a cytoscape plugin
  
• The Inner Cell Life movie - download link (large!)
  

 

Lecture slides

 

 
 

What are pathways and networks?

 

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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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http://discover.nci.nih.gov/kohnk/interaction_maps.html

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http://sugp.caltech.edu/endomes

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Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M. Nature 2002 Jan 10; 415(6868): 180-183 (Available from http://baderlab.org/Publications)

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A "pathway" is as arbitrary as our assignment of protein function, since proteins can certainly have more than one function, and be responsible for more than one phenotype

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Where is pathway information found?

 

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Pathguide: the pahway resource list

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The Cancer Cell Map

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The Cancer Cell Map

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The Cancer Cell Map

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The Cancer Cell Map

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Pathway Commons

 
 

How can we use pathway information?

 

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Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007;2(10):2366-82. PMID: 17947979
 
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003 Nov;13(11):2498-504. PMID: 14597658

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Cytoscape - biological graph visualization and analysis

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Detailed example: detecting protein complexes

 

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MCODE - a cytoscape plugin

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The Inner Cell Life movie - download link (large!)

 

 
 

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