SeptiSearch

After performing extensive literature curation of 74 sepsis-related publications involving transcriptomics, 103 unique gene sets (comprising 20,899 unique genes) from thousands of patients were collated together with associated metadata. Frequently described genes included in gene sets as well as the molecular mechanisms they were involved in were identified. These mechanisms included neutrophil degranulation, generation of second messenger molecules, IL-4 and -13 signaling, and IL-10 signaling among many others. The database, which we named SeptiSearch, is made available in a web application created using the Shiny framework in R, (available at https://septisearch.ca). CONCLUSIONS: SeptiSearch provides members of the sepsis community the bioinformatic tools needed to leverage and explore the gene sets contained in the database. This will allow the gene sets to be further scrutinized and analyzed for their enrichment in user-submitted gene expression data and used for validation of in-house gene sets/signatures.本研究针对74篇涉及转录组学的脓毒症相关文献开展了系统性梳理，整合了来自数千名患者的103个独特基因集（涵盖20899个独特基因）及其配套元数据。研究识别了基因集中高频出现的基因及其参与的分子机制，包括中性粒细胞脱颗粒、第二信使分子生成、白细胞介素-4（IL-4）与白细胞介素-13（IL-13）信号通路、白细胞介素-10（IL-10）信号通路等多种生物学过程。本研究构建了名为SeptiSearch的数据库，并基于R语言的Shiny框架开发了配套的Web应用程序，访问地址为https://septisearch.ca。结论：SeptiSearch可为脓毒症研究领域的科研人员提供所需的生物信息学工具，以利用并探索数据库中收录的基因集。这将支持研究人员对基因集进行进一步的深入审视与分析，以验证其在用户提交的基因表达数据中的富集情况，同时可用于验证自研基因集或特征标签。