GeneFriends

GeneFriends constructs and analyzes gene co-expression networks from RNA sequencing (RNA-seq) data to identify functionally related genes and prioritize candidates in human and mouse.

Key Features:

• Co-expression Network Construction: Constructs co-expression networks from RNA-seq data across 46,475 human and 34,322 mouse samples.
• Gene Prioritization: Prioritizes candidate genes using a guilt-by-association approach based on expression patterns relative to a seed list of known genes.
• Functional Annotation: Annotates poorly characterized genes by associating them with well-annotated co-expressed partners to infer possible functions.
• Updated Databases: Incorporates continually updated RNA-seq datasets to maintain current gene and transcript co-expression networks.

Scientific Applications:

• Functional Genomics: Infers functional relationships and gene regulatory mechanisms from co-expression patterns.
• Disease Research: Identifies candidate disease-associated genes by comparing expression profiles to known disease-related genes.
• Translational Research: Supports translation of co-expression-derived insights into hypotheses relevant for therapeutic strategies and drug development.

Methodology:

Uses RNA-seq data to construct gene co-expression networks and analyzes those networks under the principle that genes with similar expression patterns across conditions are likely functionally related or involved in common biological pathways.