Science

When living organisms are exposed to potentially toxic chemicals, they respond via changes in gene expression. Traditional differentially expressed gene analysis based on before/after blood samples does not reveal the response's temporal dynamics, and often produces false positives and negatives....

Mammalian animal model species for preclinical drug testing share a large number of genes with similar names and/or protein primary structures, but gene expression patterns in different tissues and in response to different drugs have not been previously systematically characterized. Here, we experimentally measure the gene expression responses (reactomes) of each gene in the mouse and rat genomes in 10 different organs to 3 different drugs. Surprisingly, we observe that gene reactomes across species generally do not correlate with structural similarity. Thus, we propose an alternative

functional cross-species gene mapping approach, based on organ-specific gene expression response

to drug dosing.

Generative pre-trained models, such as BERT and GPT, have demonstrated remarkable success in natural language processing and computer vision. Leveraging the combination of large-scale, diverse datasets, transformers...

Our contributions include a gene reactome vector prediction module, a robust framework for mapping drug-induced gene expression patterns across species, strategies for optimizing experimental design, and enhanced gene mapping precision. These advancements provide a new tool for genetic research and a new paradigm for cross-species insights, potentially revolutionizing our understanding of gene function, drug responses, and the translation of findings from model organisms to human clinical applications.