Network motifs: simple building blocks of complex networks.

@article{Milo2002NetworkMS,
  title={Network motifs: simple building blocks of complex networks.},
  author={Ron Milo and Shai S. Shen-Orr and Shalev Itzkovitz and Nadav Kashtan and Dmitri B. Chklovskii and Uri Alon},
  journal={Science},
  year={2002},
  volume={298 5594},
  pages={
          824-7
        }
}
Complex networks are studied across many fields of science. [] Key Result We found such motifs in networks from biochemistry, neurobiology, ecology, and engineering. The motifs shared by ecological food webs were distinct from the motifs shared by the genetic networks of Escherichia coli and Saccharomyces cerevisiae or from those found in the World Wide Web.

Network motif identification in stochastic networks.

A finite mixture model for stochastic networks is established and an expectation-maximization algorithm is developed for identifying Stochastic network motifs derived from families of mutually similar but not necessarily identical patterns of interconnections.

Topological generalizations of network motifs.

Using mathematical modeling, a systematic approach is presented to define "motif generalizations": families of motifs of different sizes that share a common architectural theme in transcription, neuronal, and electronic networks.

Formal Analysis of Network Motifs Links Structure to Function in Biological Programs

This work demonstrates the scalability and biological relevance of the approach by studying the previously defined networks governing myeloid differentiation, the yeast cell cycle, and naïve pluripotency in mouse embryonic stem cells, revealing the requirement for certain motifs in these systems.

Organisation of feed-forward loop motifs reveals architectural principles in natural and engineered networks

It is shown how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli and have implications for understanding how networked systems are constructed from motif parts and elucidates constraints that guide their evolution.

On motifs and functional modules in complex networks

  • Jun WangG. Provan
  • Biology
    2009 IEEE Toronto International Conference Science and Technology for Humanity (TIC-STH)
  • 2009
It is argued that the over-representation of motifs arises not because motifs are fundamental network fragments, but as a result of predesigned basic functional modules consisting of motif-clusters, and cross-module connections involving buses in the circuits and global regulators in the transcriptional regulatory network.

An Algorithm to Construct Network Motifs for Bioinformatics Study

This paper proposes a systematic method which can generate all the allowed network motifs without bipartite, isolated and isomorphic motifs and illustrated its approach by applying it to generate the complete sets of both 3-node-motifs and 4- node-Motifs.

Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks

Methods to decipher the rules controlling how small structures cluster and connect in complex networks are developed and shown how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli.

In Search of the Biological Significance of Modular Structures in Protein Networks

Using computer simulation, it is demonstrated that a higher-than-expected modularity can arise during network growth through a simple model of gene duplication, without natural selection for modularity.

Recurrent Structural Motifs Reflect Characteristics of Distinct Networks

The method from Milo et al. 2002 is modified and improved to detect significantly enriched motifs in both directed and undirected networks and reveals the nature of distinct types of networks.

Formal Analysis of Network Motifs

This work demonstrates the scalability and biological relevance of the formal reasoning approach enabling the synthesis of biological networks capable of reproducing some experimentally observed behavior by revealing the requirement for certain motifs in the network governing stem cell pluripotency.
...

References

SHOWING 1-10 OF 46 REFERENCES

Network motifs in the transcriptional regulation network of Escherichia coli

This work applied new algorithms for systematically detecting network motifs to one of the best-characterized regulation networks, that of direct transcriptional interactions in Escherichia coli, and finds that much of the network is composed of repeated appearances of three highly significant motifs.

Local graph alignment and motif search in biological networks.

  • J. BergM. Lässig
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2004
A statistical model for the occurrence of topological motifs derived from families of mutually similar but not necessarily identical patterns is established, from which a scoring function for their statistical significance is derived.

Emergence of scaling in random networks

A model based on these two ingredients reproduces the observed stationary scale-free distributions, which indicates that the development of large networks is governed by robust self-organizing phenomena that go beyond the particulars of the individual systems.

Collective dynamics of ‘small-world’ networks

Simple models of networks that can be tuned through this middle ground: regular networks ‘rewired’ to introduce increasing amounts of disorder are explored, finding that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs.

Exploring complex networks

This work aims to understand how an enormous network of interacting dynamical systems — be they neurons, power stations or lasers — will behave collectively, given their individual dynamics and coupling architecture.

Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications

A detailed statistical analysis of the protein interactions in Saccharomyces cerevisiae is presented, showing the link dynamics is the dominant evolutionary force shaping the statistical structure of the network, while the slower gene duplication dynamics mainly affects its size.

The large-scale organization of metabolic networks

This analysis of metabolic networks of 43 organisms representing all three domains of life shows that, despite significant variation in their individual constituents and pathways, these metabolic networks have the same topological scaling properties and show striking similarities to the inherent organization of complex non-biological systems.

Topological and causal structure of the yeast transcriptional regulatory network

A graph of 909 genetically or biochemically established interactions among 491 yeast genes is created, showing a deviation from randomness probably reflects functional constraints that include biosynthetic cost, response delay and differentiative and homeostatic regulation.

Topology of technology graphs: small world patterns in electronic circuits.

It is conjecture that the small world pattern arises from the compact design in which many elements share a small, close physical neighborhood plus the fact that the system must define a single connected component (which requires shortcuts connecting different integrated clusters).

The structure of scientific collaboration networks.

  • M. Newman
  • Physics
    Proceedings of the National Academy of Sciences of the United States of America
  • 2001
It is shown that these collaboration networks form "small worlds," in which randomly chosen pairs of scientists are typically separated by only a short path of intermediate acquaintances.