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Learning and Inference in Computational Systems Biology

Relationship between structure and dynamics of gene regulatory networks

author: Tapesh Santra, Department of Computing Science, University of Glasgow

Description

Gene regulatory networks in living cells are comprised of recurring network motifs, which perform key functions to control cellular responses. Mathematical models of network motifs are already developed and experimentally validated. We analyze the stability of previously validated mathematical models of network motifs against the fluctuations in their associated biochemical reaction rates and find that all of these elementary functional modules are stable against any perturbation in their rates of reaction. In gene regulatory networks the motifs are connected to each other in a directed acyclic manner. Any large assembly of stable and robust motifs connected with each other in a directed acyclic manner exhibits stable and robust dynamics. All the motifs except those having feedback loops in their structure preserve certain dynamic properties when embedded within large operational networks. Our study also suggests that evolutionary mechanisms selected stable and robust functional modules with which to build regulatory networks in order to ensure stability and reliability on a larger scale instead of finding the simplest canonical representation with which to serve the same purpose.

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Slides
0:00 Relations between Structure and Dynamics of Transcription Regulatory Networks
0:00 Introduction
1:21 Structural Complexity of Gene Regulatory Network
2:32 Gene Regulatory Networks: Structural Chaos
3:11 Abstraction
4:12 Gene Regulatory Network of S. Cerevisiae
4:24 The Regulatory Network of S. Cerevisiae
4:40 Structural Properties of Yeast Regulatory Network: Network Motif Analysis - 1
6:09 Structural Properties of Yeast Regulatory Network: Network Motif Analysis - 2
6:31 Structural Properties of Yeast Regulatory Network: Network Motif Analysis - 3
7:01 The Hierarchical Structure of Yeast Regulatory Network
7:15 Properties of the Hierarchy
8:07 Dynamics
8:09 Dynamics of Network Motifs
9:11 Dynamics Of FFL Motif
9:57 Important Observations and Beyond FFL
10:37 Dynamics of Cyclic Motifs
11:31 Location of The Cyclic Structures in The Hierarchy - 1
12:45 Location of The Cyclic Structures in The Hierarchy - 2
13:10 Effect of Adding Small Feedback Loops in a Large Hierarchical Structure
16:29 Summary
17:32 Conclusion
18:18 Thank You
18:31 - Questions
20:14 - Questions
20:53 - Questions
21:44 - Questions
22:30 - Questions
22:48 - Questions

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