Interuniversity Institute of Bioinformatics Brussels

Brussels, Belgium

Interuniversity Institute of Bioinformatics Brussels

Brussels, Belgium
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Bellot P.,Polytechnic University of Catalonia | Bellot P.,University of Liège | Olsen C.,Free University of Colombia | Olsen C.,Interuniversity Institute of Bioinformatics Brussels | And 3 more authors.
BMC Bioinformatics | Year: 2015

Background: In the last decade, a great number of methods for reconstructing gene regulatory networks from expression data have been proposed. However, very few tools and datasets allow to evaluate accurately and reproducibly those methods. Hence, we propose here a new tool, able to perform a systematic, yet fully reproducible, evaluation of transcriptional network inference methods. Results: Our open-source and freely available Bioconductor package aggregates a large set of tools to assess the robustness of network inference algorithms against different simulators, topologies, sample sizes and noise intensities. Conclusions: The benchmarking framework that uses various datasets highlights the specialization of some methods toward network types and data. As a result, it is possible to identify the techniques that have broad overall performances. © 2015 Bellot et al.


Olsen C.,Free University of Colombia | Olsen C.,Interuniversity Institute of Bioinformatics Brussels | Bontempi G.,Free University of Colombia | Bontempi G.,Interuniversity Institute of Bioinformatics Brussels | And 3 more authors.
Frontiers in Genetics | Year: 2014

When inferring networks from high-throughput genomic data, one of the main challenges is the subsequent validation of these networks. In the best case scenario, the true network is partially known from previous research results published in structured databases or research articles. Traditionally, inferred networks are validated against these known interactions. Whenever the recovery rate is gauged to be high enough, subsequent high scoring but unknown inferred interactions are deemed good candidates for further experimental validation. Therefore such validation framework strongly depends on the quantity and quality of published interactions and presents serious pitfalls: (1) availability of these known interactions for the studied problem might be sparse; (2) quantitatively comparing different inference algorithms is not trivial; and (3) the use of these known interactions for validation prevents their integration in the inference procedure. The latter is particularly relevant as it has recently been showed that integration of priors during network inference significantly improves the quality of inferred networks. To overcome these problems when validating inferred networks, we recently proposed a data-driven validation framework based on single gene knock-down experiments. Using this framework, we were able to demonstrate the benefits of integrating prior knowledge and expression data. In this paper we used this framework to assess the quality of different sources of prior knowledge on their own and in combination with different genomic data sets in colorectal cancer. We observed that most prior sources lead to significant F -scores. Furthermore, their integration with genomic data leads to a significant increase in F -scores, especially for priors extracted from full text PubMed articles, known co-expression modules and genetic interactions. Lastly, we observed that the results are consistent for three different data sets: experimental knock-down data and two human tumor data sets. © 2014 Olsen, Bontempi, Emmert-Streib, Quackenbush and Haibe-Kains.


Olsen C.,Free University of Colombia | Olsen C.,Interuniversity Institute of Bioinformatics Brussels | Fleming K.,Dana-Farber Cancer Institute | Prendergast N.,Dana-Farber Cancer Institute | And 6 more authors.
Genomics | Year: 2014

Although many methods have been developed for inference of biological networks, the validation of the resulting models has largely remained an unsolved problem. Here we present a framework for quantitative assessment of inferred gene interaction networks using knock-down data from cell line experiments. Using this framework we are able to show that network inference based on integration of prior knowledge derived from the biomedical literature with genomic data significantly improves the quality of inferred networks relative to other approaches. Our results also suggest that cell line experiments can be used to quantitatively assess the quality of networks inferred from tumor samples. © 2014.


PubMed | University of Padua, Interuniversity Institute of Bioinformatics Brussels, EMBL EBI, Research and Innovation Center and 2 more.
Type: Journal Article | Journal: Nucleic acids research | Year: 2016

COLOMBOS is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. Compared to the previous version it has more than doubled in size, both in terms of species and data available. The manually curated condition annotation has been overhauled as well, giving more complete information about samples experimental conditions and their differences. Functionality-wise cross-species analyses now enable users to analyse expression data for all species simultaneously, and identify candidate genes with evolutionary conserved expression behaviour. All the expression-based query tools have undergone a substantial improvement, overcoming the limit of enforced co-expression data retrieval and instead enabling the return of more complex patterns of expression behaviour. COLOMBOS is freely available through a web application at http://colombos.net/. The complete database is also accessible via REST API or downloadable as tab-delimited text files.

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