GeneHub-GEPIS

GeneHub-GEPIS performs digital gene expression profiling by aggregating expressed sequence tag (EST) library data and EST counts to compute normalized expression levels across human and mouse normal and tumor tissues.

Key Features:

• Integrated Database: Incorporates pre-defined gene structures derived from mRNA transcript sequences sourced from major databases and cross-references common gene identifiers.
• EST-based Expression Quantification: Aggregates expressed sequence tag (EST) library information and EST counts to compute normalized gene expression levels across tissues.
• Genome-Based Mapping (GMAP): Uses GMAP to map ESTs to genomic locations and link ESTs to corresponding genes, reducing incorrect EST-gene matches and minimizing noise.
• Gene-Centric Analyses: Provides gene-centric analyses including microRNA expression analysis, basic gene annotation, and batch analysis.
• Cross-Species Linking: Links mouse and human genes to enable comparative expression analyses.
• Large-Scale Screening: Enables large-scale screening to identify tissue- and tumor-specific genes.
• GEPIS Regional Atlas: Generates a GEPIS Regional Atlas depicting expression characteristics within selected genomic regions.

Scientific Applications:

• Gene Function and Therapeutic Target Identification: Supports identification of gene function and potential therapeutic targets by profiling expression across normal and cancerous tissues.
• Tissue- and Tumor-Specific Gene Discovery: Facilitates mining of tissue- and tumor-specific genes through large-scale expression screening.
• Comparative Cross-Species Expression Analysis: Enables comparative analyses between human and mouse gene expression.
• Regional Expression Characterization: Provides regional genomic expression visualization via the GEPIS Regional Atlas.

Methodology:

Aggregates EST library information and EST counts, maps ESTs to genomic locations using GMAP against pre-defined gene structures derived from mRNA transcript sequences from major databases, and computes normalized gene expression levels across tissues.