OralExplorer

OralExplorer integrates and analyzes GEO-derived transcriptomic and single-cell sequencing data to characterize molecular mechanisms and biomarkers of oral inflammatory diseases.

Key Features:

• Data Integration and Normalization: Integrates oral inflammatory disease-related datasets from the GEO database and applies standardized normalization for consistency across analyses.
• Differential Gene Expression Analysis: Identifies genes with significant expression changes across conditions using transcriptomic datasets.
• Immune Infiltration Analysis: Examines presence and roles of immune cell types within datasets.
• Correlation Analysis: Investigates relationships between biological variables such as gene expression across samples.
• Pathway Enrichment Analysis: Performs enrichment to highlight pathways involved in disease mechanisms.
• Single-Cell Analysis: Analyzes single-cell sequencing data to assess cellular heterogeneity and produces cluster plots, feature plots, and heatmaps.
• Visualization Outputs: Generates images and detailed tables summarizing analysis results.
• Validation of Biomarkers: Identified six candidate biomarkers (IL1β, SRGN, CXCR1, FGR, ARHGEF2, PTAFR) and validated them using quantitative PCR (qPCR) and immunohistochemistry (IHC), showing higher expression in periodontitis samples.

Scientific Applications:

• Molecular characterization: Enables identification of molecular signatures and pathways underlying oral inflammatory diseases using bulk and single-cell transcriptomics.
• Biomarker discovery and validation: Supports discovery of candidate biomarkers and their experimental validation by qPCR and IHC in periodontitis samples.
• Immune and cellular heterogeneity studies: Facilitates analysis of immune infiltration and cellular heterogeneity in oral tissues.

Methodology:

Computational methods explicitly include integration of GEO datasets, standardized normalization, differential gene expression analysis, immune infiltration analysis, correlation analysis, pathway enrichment analysis, single-cell sequencing analysis with cluster plots, feature plots, and heatmaps, and generation of images and tables.