背景:口腔炎性疾病是主要由口腔病原体引起的局部感染性疾病,有可能导致严重的全身并发症。然而,这些疾病的公开数据集没有得到充分利用。为了解决这个问题,开发了一个名为OralExplorer的网络工具。该工具整合了现有数据,并提供了全面的在线生物信息学分析。
方法:从GEO数据库获得人类口腔炎性疾病相关数据集,并使用标准化过程进行标准化。然后对转录组数据进行差异基因表达分析,免疫浸润分析,相关分析,途径富集分析,和可视化。单细胞测序数据可视化为聚类图,特征图,和热图。Web平台主要是使用Shiny构建的。通过qPCR和IHC使用局部临床样品验证在OralExplorer中鉴定的生物标志物。
结果:共有35个人类口腔炎性疾病相关数据集,涵盖6种主要疾病类型和901个样本,被纳入研究,以确定口腔疾病机制的潜在分子特征。OralExplorer由5个主要分析模块(差异基因表达分析、免疫浸润分析,相关分析,途径富集分析和单细胞分析),具有多个可视化选项。该平台提供了一个简单直观的界面,用于可视化的高质量图像,和详细的分析结果表,便于用户访问。六个标记(IL1β,SRGN,CXCR1、FGR、ARHGEF2和PTAFR)由OralExplorer鉴定。基于qPCR和IHC的实验验证显示,牙周炎组中这些基因的水平明显更高。
结论:OralExplorer是口腔炎性疾病的综合分析平台。它允许用户交互式地探索这些疾病的作用和消退的分子机制。它还帮助牙科研究人员解锁与口腔疾病相关的转录组学数据的潜在价值。OralExplorer可以在https://smuonco访问。shinyapps.io/OralExplorer/(备用URL:http://robinl-lab.com/OralExplorer)。
Oral inflammatory diseases are localized infectious diseases primarily caused by oral pathogens with the potential for serious systemic complications. However, publicly available datasets for these diseases are underutilized. To address this issue, a web tool called OralExplorer was developed. This tool integrates the available data and provides comprehensive online bioinformatic analysis.
Human oral inflammatory disease-related datasets were obtained from the GEO database and normalized using a standardized process. Transcriptome data were then subjected to differential gene expression analysis, immune infiltration analysis, correlation analysis, pathway enrichment analysis, and visualization. The single-cell sequencing data was visualized as cluster plot, feature plot, and heatmaps. The web platform was primarily built using Shiny. The biomarkers identified in OralExplorer were validated using local clinical samples through qPCR and IHC.
A total of 35 human oral inflammatory disease-related datasets, covering 6 main disease types and 901 samples, were included in the study to identify potential molecular signatures of the mechanisms of oral diseases. OralExplorer consists of 5 main analysis modules (differential gene expression analysis, immune infiltration analysis, correlation analysis, pathway enrichment analysis and single-cell analysis), with multiple visualization options. The platform offers a simple and intuitive interface, high-quality images for visualization, and detailed analysis results tables for easy access by users. Six markers (IL1β, SRGN, CXCR1, FGR, ARHGEF2, and PTAFR) were identified by OralExplorer. qPCR- and IHC-based experimental validation showed significantly higher levels of these genes in the periodontitis group.
OralExplorer is a comprehensive analytical platform for oral inflammatory diseases. It allows users to interactively explore the molecular mechanisms underlying the action and regression of these diseases. It also aids dental researchers in unlocking the potential value of transcriptomics data related to oral diseases. OralExplorer can be accessed at https://smuonco.shinyapps.io/OralExplorer/ (Alternate URL: http://robinl-lab.com/OralExplorer ).