• Overview of Chaperone Networks
• 41 min
  1. Mapping the molecular chaperone interaction network in yeast

  • Prof. Walid A. Houry
• 30 min
  2. The interaction network of the GroEL chaperonin

  • Prof. Dr. F. Ulrich Hartl
• 61 min
  3. Human heat shock protein families

  • Prof. Herman Kampinga
• 42 min
  4. Extracellular proteostasis: an emerging field

  • Prof. Mark Wilson
• 36 min
  5. Protein homeostasis and the chaperone interaction network in Arabidopsis thaliana

  • Prof. Rongmin Zhao
• Proteasome Networks
• 64 min
  6. Biogenesis of the eukaryotic proteasome

  • Prof. Mark Hochstrasser
• Understanding Intrinsically Disordered Proteins in Protein Homeostasis
• 36 min
  7. Intrinsically unstructured proteins: regulation and disease

  • Dr. M. Madan Babu
• 43 min
  8. The roles of intrinsic disorder in protein interaction networks

  • Prof. Vladimir N. Uversky
• Gene Regulatory Networks and their Role in Protein Homeostasis
• 38 min
  9. Network motifs: basic building blocks of biological networks

  • Prof. Uri Alon
• 41 min
  10. Structure, evolution and dynamics of gene regulatory networks

  • Dr. M. Madan Babu
• 33 min
  11. Computational methods in analysis of gene regulation and protein interactions

  • Prof. Ron Shamir
• 51 min
  12. Protein-protein interaction networks

  • Prof. Peter Csermely
• Protein Homeostasis in the Endoplasmic Reticulum
• 56 min
  13. Role of calnexin and calreticulin in protein homeostasis within the endoplasmic reticulum

  • Prof. David B. Williams
• 30 min
  14. The unfolded protein response

  • Prof. Kazutoshi Mori
• 38 min
  15. Role of ER stress in cystic fibrosis airway inflammation

  • Dr. Carla Maria Pedrosa Ribeiro
• 57 min
  16. The recognition of misfolded glycoproteins in the endoplasmic reticulum

  • Dr. David Y. Thomas
• 49 min
  17. Chaperone systems of the endoplasmic reticulum

  • Prof. Linda M. Hendershot
• 74 min
  18. The ERAD network

  • Prof. Daniel Hebert
• Protein Homeostasis in the Mitochondria
• 22 min
  19. Protein homeostasis in mitochondria: AAA+ chaperones & proteases

  • Dr. David A. Dougan
• 46 min
  20. Protein homeostasis in mitochondria: chaperones and proteases of the mitochondrial matrix

  • Prof. Wolfgang Voos
• 26 min
  21. Mitochondrial chaperonin Hsp60: locations, functions and pathology

  • Prof. Francesco Cappello
  • Prof. Alberto J. L. Macario
• Protein Homeostasis in the Nucleus
• 23 min
  22. Nuclear protein quality control degradation

  • Dr. Richard G. Gardner
• Protein Homeostasis in Aging Disease
• 27 min
  23. Protein homeostasis during ageing: C. elegans as a model organism

  • Prof. Nektarios Tavernarakis
• Protein Homeostasis in Neurodegeneration
• 41 min
  24. Endoplasmic reticulum stress in neurodegenerative diseases

  • Prof. Claudio Soto
• 48 min
  25. Roles for Hsp40 molecular chaperones in protein misfolding disease

  • Prof. Douglas M. Cyr
• 38 min
  26. Protein folding in vivo

  • Prof. James Bardwell
• 39 min
  27. Protein degradation and defense against neurodegenerative disease 1

  • Prof. Alfred Goldberg
• 42 min
  28. Protein degradation and defense against neurodegenerative disease 2

  • Prof. Alfred Goldberg

Printable Handouts

PDF

Navigable Slide Index

1. Introduction
2. Outline
3. Finding regulatory motifs
4. Motif discovery: the two-step strategy
5. Amadeus
6. Motif search algorithm
7. Scoring over-represented motifs
8. Metazoan motif discovery benchmark
9. Comparing Amadeus to 5 popular motifs
10. Amadeus - global spatial analysis
11. Global analyses
12. Chromosomal preference in C. elegans
13. Finding transcriptional programs
14. Goal (1)
15. Our goal: bypass the two-step approach
16. Yeast osmotic shock pathway
17. 3' UTR analysis: human stem cells
18. Human stem cells: results using binned score
19. A new regulatory motif pair in C. elegans
20. Pair occurs in 154 promoters
21. Motif across the C. rhabditis genus
22. Testing the motif experimentally
23. User interface of Amadeus
24. Analysis of gene expression profiles + a network
25. Overall gene interaction network
26. Goal (2)
27. Matisse algorithm development
28. Probabilistic model
29. Front vs. back nodes
30. Test case: yeast osmotic shock
31. Pheromone response subnetwork
32. Performance comparison
33. GO and promoter analysis
34. Application to stem cells
35. Network found using Matisse
36. Accounting for PPI confidence
37. DNA damage response in S. cerevisiae
38. DNA damage response modules
39. Comparison with prior work
40. Conclusion (1)
41. Conclusion (2)
42. Thanks (1)
43. Thanks (2)

Topics Covered

• Finding regulatory motifs
• Finding motifs using target sets of promoters
• Problem definition
• The Amadeus motif finding algorithm
• Architecture, benchmark results and global analysis
• Finding transcriptional programs and their regulatory motifs
• Problem definition
• The Allegro software for recovering transcriptional program
• Results on yeast osmotic shock expression profiles
• Recovering microRNA binding motifs from 3' UTRs using stem cell expression profiles
• Discovering a novel motif pair in C. elegans
• Utilizing network information
• Using expression and protein interaction data
• Problem definition and the Matisse algorithm
• Demonstration of Matisse on yeast osmotic shock data
• Comparison of Matisse to other algorithms
• Demonstration of Matisse on human stem cell data
• The pluripotency network
• Using expression and protein interaction data with interaction confidence
• The Cezanne algorithm
• DNA damage response in yeast

Links

Series:

• Protein Homeostasis

Categories:

• Biochemistry
• Cell Biology
• Methods

Talk Citation

Publication History

• Published on February 2, 2012
• Reviewed on October 19, 2020

Financial Disclosures

• Prof. Ron Shamir has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.