RT Journal Article
SR Electronic
T1 Continuous-trait probabilistic model for comparing multi-species functional genomic data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 283093
DO 10.1101/283093
A1 Yang Yang
A1 Quanquan Gu
A1 Yang Zhang
A1 Takayo Sasaki
A1 Julianna Crivello
A1 Rachel J. O’Neill
A1 David M. Gilbert
A1 Jian Ma
YR 2018
UL http://biorxiv.org/content/early/2018/03/16/283093.abstract
AB 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.