Genevestigator

Genevestigator enables exploration and analysis of gene expression across thousands of manually curated microarray and RNAseq experiments to support biomarker discovery and systems biology investigations.

Key Features:

• Comprehensive Data Integration: Integrates thousands of manually curated microarray and RNAseq experiments across organisms and biological contexts including diseases, drugs, tissues, cancers, cell lines, and genotypes.
• Scalable Architecture and Algorithms: Employs enhanced system architecture and algorithmic improvements to handle large-scale datasets.
• Advanced Querying and Analysis: Projects user genes or datasets against reference profiles and supports context-specific expression analysis, biomarker identification, clustering of genes into expression modules, and modeling of expression responses within metabolic and regulatory networks.
• Pathway Data Curation: Includes curated pathway information for organisms such as mouse and Arabidopsis.
• Meta-Analysis and Quality Control: Performs large-scale manual curation and quality control to support meta-analysis of expression data.

Scientific Applications:

• Biomarker Discovery: Identification of biomarker genes through comparative expression analysis across conditions.
• Systems Biology and Network Modeling: Modeling and analysis of expression responses within metabolic and regulatory networks.
• Comparative Expression Profiling: Comparative analysis of gene expression across diseases, drugs, tissues, cancers, cell lines, and genotypes.
• Reference Expression Database: Serving as a reference expression database for genomics and systems biology research.
• Meta-Analysis of Large-Scale Studies: Supporting meta-analysis using manually curated and quality-controlled datasets.

Methodology:

Integration of manually curated microarray and RNAseq experiments; projection of genes/datasets against reference profiles; clustering of genes into expression modules; modeling expression responses within metabolic and regulatory networks; incorporation of curated pathway information for mouse and Arabidopsis; and large-scale manual curation and quality control enabled by enhanced system architecture and algorithmic improvements.