# Superfamilies of Evolved and Designed Networks

@article{Milo2004SuperfamiliesOE, title={Superfamilies of Evolved and Designed Networks}, author={Ron Milo and Shalev Itzkovitz and Nadav Kashtan and Reuven Levitt and Shai S. Shen-Orr and Inbal Ayzenshtat and Michal Sheffer and Uri Alon}, journal={Science}, year={2004}, volume={303}, pages={1538 - 1542} }

Complex biological, technological, and sociological networks can be of very different sizes and connectivities, making it difficult to compare their structures. Here we present an approach to systematically study similarity in the local structure of networks, based on the significance profile (SP) of small subgraphs in the network compared to randomized networks. We find several superfamilies of previously unrelated networks with very similar SPs. One superfamily, including transcription…

## 1,209 Citations

### Algorithmic complexity of motifs clusters superfamilies of networks

- Computer Science2013 IEEE International Conference on Bioinformatics and Biomedicine
- 2013

It is reported that using numerical approximations of Kolmogorov complexity, by means of algorithmic probability, clusters different classes of networks.

### Characterizing Motifs in Weighted Complex Networks

- Computer Science
- 2005

Two novel measures are presented: the intensity of a subgraph, defined as the geometric mean of its link weights, and the coherence, depicting the homogeneity of the weights, which are generalized to weighted networks using the concept of motif scores.

### Cliques and duplication–divergence network growth

- Computer ScienceNew journal of physics
- 2005

A population of complete subgraphs or cliques in a protein network model is studied and a clique population distribution is derived, which scales linearly with the size of the network and is in perfect agreement with numerical simulations.

### Classes of complex networks defined by role-to-role connectivity profiles.

- Computer ScienceNature physics
- 2007

It is reported that networks with different functions, including the Internet, metabolic, air transportation and protein interaction networks, have distinct patterns of connections among nodes with different roles, and that, as a consequence, complex networks can be classified into two distinct functional classes on the basis of their link type frequency.

### Exploring biological network structure with clustered random networks

- Computer ScienceBMC Bioinformatics
- 2009

A new Markov chain simulation algorithm is developed and implemented to generate simple, connected random graphs that have a specified degree sequence and level of clustering, but are random in all other respects, allowing for systematic study of the impacts of connectivity and redundancies on network function and dynamics.

### Property-Driven Statistics of Biological Networks

- Computer ScienceTrans. Comp. Sys. Biology
- 2006

An analysis of heterogeneous biological networks based on randomizations that preserve the structure of component subgraphs is introduced and applied to the yeast protein-protein interaction and…

### Emergence of dynamic properties in network hypermotifs

- Computer ScienceProceedings of the National Academy of Sciences of the United States of America
- 2022

This framework defines hypermotifs—arrangements of network motif assemblies and finds that each type of network is enriched in specific hyperMotifs that show new dynamic properties.

### Randomization and Feedback Properties of Directed Graphs Inspired by Gene Networks

- Computer ScienceCMSB
- 2006

A graph decimation algorithm, called “leaf-removal”, which can be used to evaluate the feedback in a random graph ensemble is reviewed, and the possibility of analyzing networks where the diagonal of the adjacency matrix is structured, that is, has a fixed number of nonzero entries is considered.

### A network model with structured nodes

- Computer SciencePhysical review. E, Statistical, nonlinear, and soft matter physics
- 2011

We present a network model in which words over a specific alphabet, called structures, are associated to each node and undirected edges are added depending on some distance measure between different…

## References

SHOWING 1-10 OF 68 REFERENCES

### Network motifs: simple building blocks of complex networks.

- BiologyScience
- 2002

Network motifs, patterns of interconnections occurring in complex networks at numbers that are significantly higher than those in randomized networks, are defined and may define universal classes of networks.

### Emergence of scaling in random networks

- Computer ScienceScience
- 1999

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.

### Specificity and Stability in Topology of Protein Networks

- BiologyScience
- 2002

It is found that for both interaction and regulatory networks, links between highly connected proteins are systematically suppressed, whereas those between a highly connected and low-connected pairs of proteins are favored.

### Classification of scale-free networks

- Computer ScienceProceedings of the National Academy of Sciences of the United States of America
- 2002

It is shown that the betweenness centrality displays a power-law distribution with an exponent η, which is robust, and is used to classify the scale-free networks, including two universality classes with η ≈ 2.2(1) and 2.0, respectively.

### The Structure and Function of Complex Networks

- Computer ScienceSIAM Rev.
- 2003

Developments in this field are reviewed, including such concepts as the small-world effect, degree distributions, clustering, network correlations, random graph models, models of network growth and preferential attachment, and dynamical processes taking place on networks.

### Network motifs in the transcriptional regulation network of Escherichia coli

- Computer ScienceNature Genetics
- 2002

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.

### Exploring complex networks

- BiologyNature
- 2001

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 function of the feed-forward loop network motif

- Computer ScienceProceedings of the National Academy of Sciences of the United States of America
- 2003

This study defines the function of one of the most significant recurring circuit elements in transcription networks, the feed-forward loop (FFL), which is a three-gene pattern composed of two input transcription factors, both jointly regulating a target gene.

### From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli.

- BiologyBioEssays : news and reviews in molecular, cellular and developmental biology
- 1998

This paper presents a global characterization of the transcriptional regulation in Escherichia coli on the basis of the current data, with special emphasis given to circular sequences of interactions ("circuits") because of their critical dynamical properties.

### The small world of human language

- LinguisticsProceedings of the Royal Society of London. Series B: Biological Sciences
- 2001

It is shown that graphs of words in sentences display two important features recently found in a disparate number of complex systems, the so called small–world effect and a scale–free distribution of degrees.