


 

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] ShenOrr SS, Milo R, Mangan S, Alon U: Network motifs in the
transcriptional network of Escherichia coli. Nat Genet 2002, 31:6468
[link]
[2] E. coli transcription networks [link]
[3] Milo R, ShenOrr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U:
Network Motifs: Simple Building Blocks of Complex Networks.
Science 2002, 298:824827. [link]
[4] Yeast transcription network [link]
[5]
Watts, D. and Strogatz, S.: Collective dynamics of 'smallworld' 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]

 

 
