Topological effects of data incompleteness of gene regulatory networks

Joaquin Sanz, Emanuele Cozzo, Javier Borge-Holthoefer, Yamir Moreno

Research output: Contribution to journalArticle

5 Citations (Scopus)

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.

Original languageEnglish
Article number110
JournalBMC Systems Biology
Volume6
DOIs
Publication statusPublished - 25 Aug 2012
Externally publishedYes

Fingerprint

Incompleteness
Gene Regulatory Networks
Regulatory Networks
Gene Regulatory Network
Electric network analysis
Bacteria
Genes
Bacterial Genes
Unknown
Biological Networks
Modularity
Uncertainty
Completeness
Pathway
Gene

Keywords

  • Biological networks
  • Community structure
  • Motifs significance
  • Network superfamilies
  • Transcriptional regulatory networks

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology
  • Applied Mathematics
  • Modelling and Simulation
  • Computer Science Applications

Cite this

Topological effects of data incompleteness of gene regulatory networks. / Sanz, Joaquin; Cozzo, Emanuele; Borge-Holthoefer, Javier; Moreno, Yamir.

In: BMC Systems Biology, Vol. 6, 110, 25.08.2012.

Research output: Contribution to journalArticle

Sanz, Joaquin ; Cozzo, Emanuele ; Borge-Holthoefer, Javier ; Moreno, Yamir. / Topological effects of data incompleteness of gene regulatory networks. In: BMC Systems Biology. 2012 ; Vol. 6.
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