MSdb

MSdb integrates and standardizes next-generation sequencing (NGS) datasets and manually curated phenotype data to enable analysis of gene and miRNA expression in the human musculoskeletal system.

Key Features:

• Integrated Data Repository: Consolidates NGS datasets related to the human musculoskeletal system into a single, standardized collection.
• Visualization and Analysis of Expression: Provides visualization capabilities for metadata, gene expression, and miRNA expression at the sample level.
• Cross-Sample and Cross-Omics Analysis: Supports integrated analyses across samples and omics layers, including identification of differentially expressed genes and microRNAs.
• Network and Regulatory Analyses: Enables construction of miRNA–gene networks and gene regulatory network analyses.
• Single-Cell RNA-seq Integration: Integrates single-cell RNA sequencing (scRNA-seq) data for cross-sample and disease-specific cellular analyses.
• Manually Curated Phenotype Data: Incorporates manually curated patient phenotype information to provide clinical context for molecular data.

Scientific Applications:

• Mechanistic studies: Investigation of pathological mechanisms underlying musculoskeletal (MSK) disorders via gene and miRNA expression and regulatory networks.
• Biomarker discovery: Identification of candidate biomarkers through differential expression analyses across samples and conditions.
• Therapeutic target identification: Prioritization of potential therapeutic targets by integrating expression changes with miRNA–gene and regulatory network information.
• Cellular heterogeneity analysis: Characterization of cellular heterogeneity and disease-associated cell states using integrated scRNA-seq data.

Methodology:

Standardized processing and systematic categorization of NGS datasets; integration of NGS and scRNA-seq data; differential expression analysis for genes and microRNAs; construction of miRNA–gene networks and gene regulatory network analyses; incorporation of manually curated phenotype information.