GREIN

GREIN provides standardized re-analysis of RNA sequencing (RNA-seq) datasets from the Gene Expression Omnibus (GEO) to enable differential expression analysis, statistical power assessment, functional characterization, and connectivity analysis with LINCS L1000.

Key Features:

• Back-end computational pipeline: Uniformly processes and standardizes RNA-seq datasets from GEO.
• Extensive pre-processed dataset repository: Includes over 6,500 pre-processed RNA-seq datasets from GEO.
• Sub-setting and data export: Supports sub-setting of processed data and downloading of processed datasets.
• Visualization of gene expression: Provides visualization of gene expression patterns across samples and conditions.
• Statistical power analysis: Performs statistical power analyses to assess experimental design robustness.
• Differential gene expression signature construction and analysis: Constructs and analyzes differential gene expression signatures.
• Functional characterization: Facilitates functional characterization of gene expression changes.
• Connectivity analysis with LINCS L1000: Enables connectivity analyses integrating results with the LINCS L1000 dataset.

Scientific Applications:

• Validation and replication studies: Re-analyzes GEO RNA-seq data to validate and replicate findings across independent datasets.
• Meta-analysis: Combines multiple GEO RNA-seq datasets for meta-analytic comparison and synthesis.
• Hypothesis exploration using existing data: Enables exploration of novel hypotheses by mining pre-existing RNA-seq datasets.
• Functional genomics studies: Supports functional genomics investigations to interpret gene expression dynamics and biological implications.

Methodology:

The back-end pipeline uniformly processes and standardizes GEO RNA-seq datasets; analysis methods explicitly include statistical power analysis, differential gene expression signature construction and analysis, functional characterization, and connectivity analysis with LINCS L1000.