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Open Access Research article

Topological effects of data incompleteness of gene regulatory networks

Joaquin Sanz12, Emanuele Cozzo12, Javier Borge-Holthoefer1 and Yamir Moreno12*

Author affiliations

1 Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza 50009, Spain

2 Department of Theoretical Physics, University of Zaragoza, Zaragoza 50009, Spain

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Citation and License

BMC Systems Biology 2012, 6:110  doi:10.1186/1752-0509-6-110

Published: 25 August 2012

Abstract

Background

The topological analysis of biological networks has been a prolific topic in network science during the last decade. A persistent problem with this approach is the inherent uncertainty and noisy nature of the data. One of the cases in which this situation is more marked is that of transcriptional regulatory networks (TRNs) in bacteria. The datasets are incomplete because regulatory pathways associated to a relevant fraction of bacterial genes remain unknown. Furthermore, direction, strengths and signs of the links are sometimes unknown or simply overlooked. Finally, the experimental approaches to infer the regulations are highly heterogeneous, in a way that induces the appearance of systematic experimental-topological correlations. And yet, the quality of the available data increases constantly.

Results

In this work we capitalize on these advances to point out the influence of data (in)completeness and quality on some classical results on topological analysis of TRNs, specially regarding modularity at different levels.

Conclusions

In doing so, we identify the most relevant factors affecting the validity of previous findings, highlighting important caveats to future prokaryotic TRNs topological analysis.

Keywords:
Biological networks; Transcriptional regulatory networks; Motifs significance; Community structure; Network superfamilies