Large-scale analysis of the human and mouse transcriptomes

TLDR

High‑throughput gene expression profiling is a key tool for studying transcriptional activity across diverse biological samples, yet most studies focus on specific processes and perturbations. The authors aim to use the dataset to demonstrate mining methods and uncover insights into gene function, transcriptional regulation, disease etiology, and comparative genomics, while also providing a free public resource. They profiled 91 human and mouse samples from diverse tissues, organs, and cell lines, and created a free website for data visualization and annotation curation. The resulting dataset, covering 91 human and mouse samples from normal physiological states, provides a substantial baseline of the mammalian transcriptome and demonstrates methods for mining gene function, regulation, disease etiology, and comparative genomics.

Abstract

High-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we have generated and analyzed gene expression from a set of samples spanning a broad range of biological conditions. Specifically, we profiled gene expression from 91 human and mouse samples across a diverse array of tissues, organs, and cell lines. Because these samples predominantly come from the normal physiological state in the human and mouse, this dataset represents a preliminary, but substantial, description of the normal mammalian transcriptome. We have used this dataset to illustrate methods of mining these data, and to reveal insights into molecular and physiological gene function, mechanisms of transcriptional regulation, disease etiology, and comparative genomics. Finally, to allow the scientific community to use this resource, we have built a free and publicly accessible website ( http://expression.gnf.org ) that integrates data visualization and curation of current gene annotations.