TY - JOUR T1 - Continuous-trait probabilistic model for comparing multi-species functional genomic data JF - bioRxiv DO - 10.1101/283093 SP - 283093 AU - Yang Yang AU - Quanquan Gu AU - Yang Zhang AU - Takayo Sasaki AU - Julianna Crivello AU - Rachel J. O’Neill AU - David M. Gilbert AU - Jian Ma Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/03/16/283093.abstract N2 - 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. ER -