Stress Mice Portal. A gene expression atlas for different kinds of stress in mice brains http://hpc-bioinformatics.cineca.it/stress_mice/

Stressful experiences are part of everyday life and organisms have evolved physiological and behavioural responses aimed at coping with stress and maintain homeostasis. However, repeated or intense stress can induce maladaptive reactions leading to depression, anxiety or post-traumatic stress disorder. Functional and structural adaptations in the brain mediated by changes in gene expression, have a crucial role in the stress response. Recent years have seen a tremendous increase in scientific publications studying the transcriptional effects of several stressors on different areas of the brain. The input raw data of these studies are freely available on public repositories, such as Sequence Read Archive (SRA) operated by the National Center for Biotechnology Information (NCBI). These data represent a wealth of information for further global and integrative retrospective analyses. In order to identify convergent biological processes and signalling pathways affected by stress, and reveal possible novel candidate genes, we analyzed the RNA-seq transcriptomes obtained from the brain of mice exposed to different kinds of stress protocols. Thus we surveyed 18 published RNA-seq transcriptomic experiments obtained from SRA, whose detailed information are available here. Since each of the laboratories producing these 18 datasets analyzed their own data by following different protocols (e.g. in terms of adopted bioinformatic workflows, software, genomic versions, thresholds of significance), we re-analyzed the data by applying the same up-to-date transcriptomic computational workflow to the whole dataset in order to obtain a more comparable set of results. The results were systematized into this web portal for allowing an easy visualization, comparison, interrogation and downloading. Stress Mice Portal is a free, open-source, curated web server able to query stress-related differentially expressed genes (DEGs) using different criteria (please refer to the Help page or the paper for further information). This portal provides new insights into the transcriptional landscape of the mouse brain under several stress conditions and is useful for identifying factors contributing to vulnerability or resilience to stress.