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Latest revision as of 18:28, 9 December 2007

    (Previous lecture) ... (Next lecture)



 

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



 

Lecture slides


 



 
 

What are pathways and networks?


 

Slide 004
Lecture 23, Slide 004
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Lecture 23, Slide 005
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Lecture 23, Slide 006
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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Lecture 23, Slide 007
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Lecture 23, Slide 009
http://sugp.caltech.edu/endomes
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Lecture 23, Slide 010
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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Lecture 23, Slide 011
Slide 012
Lecture 23, Slide 012
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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Lecture 23, Slide 013
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Lecture 23, Slide 014
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Lecture 23, Slide 015



 
 

Where is pathway information found?


 

Slide 017
Lecture 23, Slide 017
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Lecture 23, Slide 018
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Lecture 23, Slide 026
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Lecture 23, Slide 027
Slide 028
Lecture 23, Slide 028
The Cancer Cell Map
Slide 029
Lecture 23, Slide 029
The Cancer Cell Map
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Lecture 23, Slide 030
The Cancer Cell Map
Slide 031
Lecture 23, Slide 031
The Cancer Cell Map
Slide 032
Lecture 23, Slide 032
Pathway Commons



 
 

How can we use pathway information?


 

Slide 034
Lecture 23, Slide 034
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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Lecture 23, Slide 047



 
 

Detailed example: detecting protein complexes


 

Slide 049
Lecture 23, Slide 049
Slide 050
Lecture 23, Slide 050
MCODE - a cytoscape plugin
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Lecture 23, Slide 051
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Lecture 23, Slide 052
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Lecture 23, Slide 053
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