title: DynOmics to identify delays and co-expression patterns across time course experiments.
abstract: Dynamic changes in biological systems can be captured by measuring molecular expression from different levels (e.g., genes and proteins) across time. Integration of such data aims to identify molecules that show similar expression changes over time; such molecules may be co-regulated and thus involved in similar biological processes. Combining data sources presents a systematic approach to study molecular behaviour. It can compensate for missing data in one source, and can reduce false positives when multiple sources highlight the same pathways. However, integrative approaches must accommodate the challenges inherent in 'omics' data, including high-dimensionality, noise, and timing differences in expression. As current methods for identification of co-expression cannot cope with this level of complexity, we developed a novel algorithm called DynOmics. DynOmics is based on the fast Fourier transform, from which the difference in expression initiation between trajectories can be estimated. This delay can then be used to realign the trajectories and identify those which show a high degree of correlation. Through extensive simulations, we demonstrate that DynOmics is efficient and accurate compared to existing approaches. We consider two case studies highlighting its application, identifying regulatory relationships across 'omics' data within an organism and for comparative gene expression analysis across organisms.
authors.affiliation: QFAB@QCIF Bioinformatics, Institute for Molecular Biosciences, The University of Queensland, Queensland Bioscience Precinct, St Lucia, QLD, Australia.|The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.
authors.forename: Jasmin
authors.initials: J
authors.lastname: Straube
authors.affiliation: Janssen Research &Development, LLC, Discovery Sciences, Menlo Park, USA.
authors.forename: Bevan Emma
authors.initials: BE
authors.lastname: Huang
authors.affiliation: The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.
authors.forename: Kim-Anh Lê
authors.initials: KL
authors.lastname: Cao