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1. Introduction
2. Two kinds of biological networks (1)
3. Two kinds of biological networks (2)
4. Protein interaction networks
5. Yeast 2-hybrid assay
6. Protien interaction network in yeast
7. Some limitations
8. Mathematical underpinnings of biological networks
9. Graphs are everywhere
10. Characterisation of graphs
11. Graphs can be represented by matrices
12. Matrix of shortest paths
13. Connectivity
14. The degrees of nodes in a graph may be correlated
15. Graph compactness
16. A measure of node and edge centrality
17. Locally dense neighborhoods of nodes in a graph
18. The best-studied mathematical models of graphs
19. A motif is a local pattern of connections in a graph
20. Broad tailed degree distributions
21. Protein interaction networks are disassortative (1)
22. Protein interaction networks are disassortative (2)
23. Affinity chromatography and protein complexes
24. Computational analysis of protein complexes
25. Hypergraphs for large sets of protein complexes
26. Protein microarrays
27. A protein kinase network
28. Transcriptional regulation networks
29. ChIP-chip
30. Autoregulatory cycles in yeast
31. Autoregulatory cycles in E. coli
32. High network compactness in E.Coli
33. Multiple small gene circuit motifs
34. Evolutionary origins of abundant circuit motifs
35. Metabolic networks
36. A metabolic network is a set of chemical reactions
37. Graphes represent chemical reaction networks
38. Graph representation of yeast metabolic network
39. Small-world graphs
40. Metabolic networks are small-world networks
41. Many graphs have "small-world" features
42. Why are metabolic networds small-world networks?
43. Limitations of graph-based analysis
44. Distribution of metabolic fluxes in E. coli
45. Flux balance analysis (1)
46. Flux balance analysis (2)
47. Region of allowable steady-state metabolic fluxes
48. A simple chemical reaction network
49. A simple chemical reaction network - steady state
50. Example questions for flux balance analysis
51. Summary (1)
52. Summary (2)
53. Appendix

Topics Covered

• Biological networks: small networks dedicated to a specific task and genome-scale networks
• Protein interaction networks
• The yeast two-hybrid assay and its limitations
• Graph theory: degree distribution and correlation, characteristic path lengths and diameter, clustering coefficient, abundance of motifs and indicators of modularity
• Measures of node and edge centrality
• Affinity chromatography
• Hypergraphs
• Protein microarrays
• Transcription regulation networks
• Metabolic networks
• Small-world networks
• Flux balance analysis

Links

Series:

• Using Bioinformatics in the Exploration of Genetic Diversity

Categories:

• Biochemistry
• Cell Biology
• Metabolism & Nutrition
• Methods

Talk Citation

Wagner, A. (2007, October 1). Analysis of protein-protein interaction, transcriptional regulation and metabolic networks [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved November 14, 2024, from https://doi.org/10.69645/OZEY5674.
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Publication History

• Published on October 1, 2007
• Archived on May 31, 2018

Financial Disclosures

• Dr. Andreas Wagner has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.