title: Effect of database drift on network topology and enrichment analyses: a case study for RegulonDB.
abstract: RegulonDB is a database storing the biological information behind the transcriptional regulatory network (TRN) of the bacterium Escherichia coli. It is one of the key bioinformatics resources for Systems Biology investigations of bacterial gene regulation. Like most biological databases, the content drifts with time, both due to the accumulation of new information and due to refinements in the underlying biological concepts. Conclusions based on previous database versions may no longer hold. Here, we study the change of some topological properties of the TRN of E. coli, as provided by RegulonDB across 16 versions, as well as a simple index, digital control strength, quantifying the match between gene expression profiles and the transcriptional regulatory networks. While many of network characteristics change dramatically across the different versions, the digital control strength remains rather robust and in tune with previous results for this index. Our study shows that: (i) results derived from network topology should, when possible, be studied across a range of database versions, before detailed biological conclusions are derived, and (ii) resorting to simple indices, when interpreting high-throughput data from a network perspective, may help achieving a robustness of the findings against variation of the underlying biological information. Database URL: www.regulondb.ccg.unam.mx.
authors.affiliation: Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, Bremen 28759, Germany and Bioinformatics Group, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, Berlin 14195, Germany m.huett@jacobs-university.de.
authors.forename: Moritz E
authors.initials: ME
authors.lastname: Beber
authors.affiliation: Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, Bremen 28759, Germany and.
authors.forename: Georgi
authors.initials: G
authors.lastname: Muskhelishvili
authors.affiliation: Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, Bremen 28759, Germany and m.huett@jacobs-university.de.
authors.forename: Marc-Thorsten
authors.initials: MT
authors.lastname: Hütt
mesh_terms: D002875:Chromosomes / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D030562:Databases, Protein; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D020411:Oligonucleotide Array Sequence Analysis; D011381:Programming Languages; D025941:Protein Interaction Mapping; D018085:Regulon; D014158:Transcription, Genetic