title: Breaking free from the chains of pathway annotation: de novo pathway discovery for the analysis of disease processes.
abstract: Interpreting the biological implications of high-throughput experiments such as gene-expression studies, genome-wide association studies and large-scale sequencing studies is not trivial. Gene-set and pathway analyses are useful tools to support the interpretation of such experiments, but rely on curated pathways or gene sets. The recent development of de novo pathway discovery methods aims to overcome this limitation. This article provides an overview of the methods currently available and reviews the advantages and challenges of this approach. In detail, it highlights the particular issues of de novo pathway discovery based on genome-wide association studies data, for which multiple different strategies have been proposed.
authors.affiliation: Bioinformatics Group, Department of Medical & Molecular Genetics, 8th Floor Tower Wing Guy's Hospital, London SE1 9RT, UK.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Lehne
authors.forename: Thomas
authors.initials: T
authors.lastname: Schlitt
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D015870:Gene Expression; D053263:Gene Regulatory Networks; D055106:Genome-Wide Association Study; D006801:Humans; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D012984:Software