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Example Networks

DiVa online is delivering 3 example networks to facilitate the first steps to usage. The first example network represents transcriptional regulation in Escherichia coli (E. coli) based on experimentally verified interactions [1]. The E. coli network is available at [2].

The second example network denotes transcriptional regulation in the yeast Saccharomyces cerevisiae (S. cerevisiae) based on experimentally verified interactions [3]. The S. cerevisiae network is available at [4].

The third example is the neuronal connectivity network of a simple multicellular organism, i.e. the nematode Caenorhabditis elegans (C. elegans) [5].

Some of the results obtained from DiVa online when using these networke were already published. In particular, this applies to the knockout of vertices [6] and the topological significance of network patterns made up of 3 vertices [7].

[1] Shen-Orr SS, Milo R, Mangan S, Alon U: Network motifs in the transcriptional network of Escherichia coli. Nat Genet 2002, 31:64-68 [link]

[2] E. coli transcription networks [link]

[3] Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U: Network Motifs: Simple Building Blocks of Complex Networks. Science 2002, 298:824-827. [link]

[4] Yeast transcription network [link]

[5] Watts, D. and Strogatz, S.: Collective dynamics of 'small-world' networks. Nature 1998, 393:440 - 442 [link]

[6] Potapov, A. P., Goemann, B. and Wingender, E.: The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks.
  BMC Bioinformatics 2008, 9:227 [link]

[7] Goemann, B., Wingender, E. and Potapov, A. P.: An approach to evaluate the topological significance of motifs and other patterns in regulatory networks. BMC Syst. Biol. 2009, 3:53 [link]

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...::: Department of Bioinformatics, Center of Informatics,Statistics and Epidemiology UMG, University of Göttingen :::...