New strategy for the representation and the integration of biomolecular knowledge at a cellular scale

Nucleic Acids Research
Roland BarriotAntoine de Daruvar

Abstract

The combination of sequencing and post-sequencing experimental approaches produces huge collections of data that are highly heterogeneous both in structure and in semantics. We propose a new strategy for the integration of such data. This strategy uses structured sets of sequences as a unified representation of biological information and defines a probabilistic measure of similarity between the sets. Sets can be composed of sequences that are known to have a biological relationship (e.g. proteins involved in a complex or a pathway) or that share similar values for a particular attribute (e.g. expression profile). We have developed a software, BlastSets, which implements this strategy. It exploits a database where the sets derived from diverse biological information can be deposited using a standard XML format. For a given query set, BlastSets returns target sets found in the database whose similarity to the query is statistically significant. The tool allowed us to automatically identify verified relationships between correlated expression profiles and biological pathways using publicly available data for Saccharomyces cerevisiae. It was also used to retrieve the members of a complex (ribosome) based on the mining of expression...Continue Reading

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Citations

Feb 3, 2005·Nature Reviews. Drug Discovery·David B Searls
Oct 19, 2006·Bioinformatics·Nicolas Goffard, Georg Weiller
Jun 8, 2013·Bioinformatics·Alberto RezolaFrancisco J Planes
Apr 27, 2010·Molecular Biology and Evolution·Kyung Mo Kim, Gustavo Caetano-Anollés
Apr 4, 2007·Nucleic Acids Research·Steven Van VoorenYves Moreau
Jun 26, 2007·Nucleic Acids Research·Nicolas Goffard, Georg Weiller
Jun 28, 2007·Genome Biology·Jean-Marc SchwartzMinoru Kanehisa
Oct 18, 2006·Proteomics·Sandrine Palcy, Eric Chevet
Mar 15, 2014·Briefings in Bioinformatics·Alberto RezolaFrancisco J Planes

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