Year: 2018
Type: preprint
Abstract: Summary A large amount of multi-species functional genomic data from high-throughput assays are becoming available to help understand the molecular mechanisms for phenotypic diversity across species. However, continuous-trait probabilistic models, which are key to such comparative analysis, remain underexplored. Here we develop a new model, called phylogenetic hidden Markov Gaussian processes (Phylo-HMGP), to simultaneously infer heterogeneous evolutionary states of functional genomic features in a genome-wide manner. Both simulation studies and real data application demonstrate the effectiveness of Phylo-HMGP. Importantly, we applied Phylo-HMGP to analyze a new cross-species DNA replication timing (RT) dataset from the same cell type in five primate species (human, chimpanzee, orangutan, gibbon, and green monkey). We demonstrate that our Phylo-HMGP model enables discovery of genomic regions with distinct evolutionary patterns of RT. Our method provides a generic framework for comparative analysis of multi-species continuous functional genomic signals to help reveal regions with conserved or lineage-specific regulatory roles.
DOI: 10.1101/283093
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Awards: III: Small: Collaborative Research: High-Dimensional Machine Learning Methods for Personalized Cancer Genomics, CAREER: Computational Methods for Analyzing Large-Scale Genomic Changes in Mammalian Genomes, G3728067801, Combined Cytological, Genomic, and Functional Mapping of Nuclear Genome Organization, G5435736845, Computational Methods for Next-Generation Comparative Genomics, G6213125703, ABI Innovation: New Software Tools for Genome Comparisons of Non-Model Organisms, G8148301435, G8859767233, G8920915315, cis-Acting Elements Regulating Developmental Control of Replication Timing
OpenAlex ID: W2789324785