Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network Ideker et...
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Integrated Genomic and Proteomic Analyses of aSystematically Perturbed Metabolic Network
Ideker et al. (2001)
Feynman Liang
Amherst College
April 2, 2014
Feynman Liang (AC) Ideker et al. (2001) April 2, 2014 1 / 10
Overview
1 Define an initial model drawn from previous research
2 Systematically perturb each pathway component genetically andenvironmentally
3 Integrate observations with pathway-specific model and globalinteraction network
4 Formulate new hypotheses and design additional pertubations to test
Feynman Liang (AC) Ideker et al. (2001) April 2, 2014 2 / 10
Initial model
Figure 1: Solid lines indicate model of galactose utilization derived from priorresearch
Feynman Liang (AC) Ideker et al. (2001) April 2, 2014 3 / 10
Response of pathway genes
Figure 2: B: Predicted and observed mRNA expression profiles, D: doubling times
Feynman Liang (AC) Ideker et al. (2001) April 2, 2014 4 / 10
Expression profile hierarchical-clustering
Figure 5: Clustering tree constructed using l2-metric of pertubation expressionprofile. Dotted lines indicate additional experiments.
Feynman Liang (AC) Ideker et al. (2001) April 2, 2014 5 / 10
Global mRNA response to pertubations
Figure 2: Gene clusters obtained by training self-organizing map on expressionprofiles
Feynman Liang (AC) Ideker et al. (2001) April 2, 2014 6 / 10
Post-transcription
Figure 3: Protein expression and mRNA change between wt+gal and wt-gal
Feynman Liang (AC) Ideker et al. (2001) April 2, 2014 7 / 10
Integration with global interaction network
Figure 4: Node greyscale intensity: ∆mRNA, yellow: protein→DNA, blue:protein-protein
Feynman Liang (AC) Ideker et al. (2001) April 2, 2014 8 / 10
References
Trey Ideker et al.
Integrated Genomic and Proteomic Analyses of a Systematically PerturbedMetabolic Network
Science 292, 929 (2001)
Feynman Liang (AC) Ideker et al. (2001) April 2, 2014 9 / 10
The End
Feynman Liang (AC) Ideker et al. (2001) April 2, 2014 10 / 10