Reconstruction of cellular signalling networks and analysis of their properties

  title={Reconstruction of cellular signalling networks and analysis of their properties},
  author={Jason A. Papin and Tony Hunter and Bernhard O. Palsson and Shankar Subramaniam},
  journal={Nature Reviews Molecular Cell Biology},
The study of cellular signalling over the past 20 years and the advent of high-throughput technologies are enabling the reconstruction of large-scale signalling networks. After careful reconstruction of signalling networks, their properties must be described within an integrative framework that accounts for the complexity of the cellular signalling network and that is amenable to quantitative modelling. 

Towards genome-scale signalling-network reconstructions

Now that the authors can simultaneously measure a substantial portion of the molecular components of a cell, they can begin to develop and test systems-level models of cellular signalling and regulatory processes, therefore gaining insights into the 'thought' processes of acell.

Modular analysis of signal transduction networks

The mechanisms that cells have developed to process information are described, and the decomposition of signalling networks into subsystems is discussed, and some simple criteria for the analysis of the resulting units are introduced.

Strategies to Investigate Signal Transduction Pathways with Mathematical Modelling

This book chapter discusses the elements of a systems biology methodology for the investigation of cell signalling systems and illustrates it with a number of examples.

A Systems Perspective of Signalling Networks in Host–Pathogen Interactions

Some of the widely used modelling methods for studying signalling pathways and their networks are described and a number of example cases are described, which provide a glimpse of the different types of insights provided by such models.

Modelling of signal transduction in yeast – sensitivity and model analysis

Modelling principles, results and open questions exemplified for a model organism, the yeast Saccharomyces cerevisiae, demonstrate some basic principles of signal transduction and signal processing and sensitivity and robustness of information perception and cellular response.

Pattern recognition of gene expression data on signalling networks of cancer

A network based analysis has been done to compare the different network properties between the normal and cancer cells using several cancer gene expression datasets and shows that the cancer signalling network is more differentiated and much more interconnected when compared to the normal cells.

Mathematical Tools in Cancer Signalling Systems Biology

Systems biology is described as a flexible approach in which the modelling strategy used depends on a trade-off between the nature of the biochemical network investigated, the biomedical question to be elucidated, and the quantity (and quality) of the experimental data available.

Modelling spatio-temporal interactions within the cell

The capability and limitations of the approaches used to study spatio-temporal dynamics of cell signalling components and how such models can be used to understand biological specificity in functional responses are described.



Overview of the Alliance for Cellular Signaling

The Alliance for Cellular Signaling will study intensively in two cells — B lymphocytes (the cells of the immune system) and cardiac myocytes — to facilitate quantitative modelling.

Navigating the signalling network in mouse cardiac myocytes

Cardiac myocytes have a complex network of signals that regulates their essential role in the rhythmic pumping of the heart. This network is an appealing model system in which to study the basic

Complexity in biological signaling systems.

The origins of the complex behavior of signaling networks and analytical approaches to deal with the emergent complexity are discussed here.

From molecular to modular cell biology

General principles that govern the structure and behaviour of modules may be discovered with help from synthetic sciences such as engineering and computer science, from stronger interactions between experiment and theory in cell biology, and from an appreciation of evolutionary constraints.

Lethality and centrality in protein networks

It is demonstrated that the phenotypic consequence of a single gene deletion in the yeast Saccharomyces cerevisiae is affected to a large extent by the topological position of its protein product in the complex hierarchical web of molecular interactions.

The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks

The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways intended both to serve the growing field of chemical-reaction level simulation of signaling networks, and to anticipate issues in large-scale data management for signaling chemistry.

Dynamical and integrative cell signaling: challenges for the new biology

Combining the dynamical view of rapidly evolving responses and the structural view arising from high‐throughput analyses of the interacting species will be the best approach toward efforts toward greater understanding of intracellular signaling processes.

Automated modelling of signal transduction networks

A computational approach for generating static models of signal transduction networks which utilizes protein-interaction maps generated from large-scale two-hybrid screens and expression profiles from DNA microarrays, and shows that the technique accurately reconstructs MAP Kinase signaling networks in Saccharomyces cerevisiae.

Modular organization of cellular networks

This work investigated the organization of interacting proteins and protein complexes into networks of modules and identified module-organizer proteins and module-connector proteins that suggest that they are important for module function and intermodule communication.