R2 platform

R2 platform provides analysis and visualization of high-throughput (HT) genomic data to support biomedical research and discovery.

Key Features:

• Comprehensive Database: Hosts both publicly accessible and shielded datasets with unified gene annotation and contains over 60,000 HT samples in the public section.
• Diverse Data Integration: Supports microarray, RNA-seq, aCGH, SNP, ChIP, methylation, miRNA, and NGS whole genome sequencing for integrated analyses.
• Interconnected Analyses: Provides correlation studies, differential expression analysis, gene set evaluations, gene ontology assessments, transcription factor binding site identification, principal component analysis (PCA), k‑means clustering, Kaplan–Meier survival scans, and signature creation.
• Advanced Visualizations: Produces gene-oriented plots, heatmaps, circos diagrams, embedded genome browser views, and Venn diagrams.

Scientific Applications:

• Integrative Genomics: Enables cross-platform and cross-dataset analyses combining microarray, RNA‑seq, aCGH, SNP, ChIP, methylation, miRNA, and whole-genome sequencing data.
• Biomarker and Signature Discovery: Supports differential expression, correlation analyses, and signature creation for biomarker identification.
• Survival Analysis: Facilitates Kaplan–Meier survival scans to associate molecular features with clinical outcomes.
• Regulatory and Functional Analysis: Supports transcription factor binding site identification and gene ontology assessments to investigate regulatory mechanisms and gene function.
• Analysis of Restricted Data: Enables analysis of both public and shielded (restricted) datasets for collaborative and unpublished data investigations.

Methodology:

Computational methods explicitly include correlation analysis, differential expression analysis, gene set and gene ontology evaluations, transcription factor binding site identification, principal component analysis (PCA), k‑means clustering, Kaplan–Meier survival scans, signature creation, and visualization generation (heatmaps, circos diagrams, embedded genome browser views, and Venn diagrams).