EnrichmentBrowser

EnrichmentBrowser performs enrichment analysis of gene expression datasets by integrating set-based and network-based methodologies to identify differentially regulated gene sets and biological pathways.

Key Features:

• Set-Based and Network-Based Analysis: Combines set-based and network-based analytical approaches to enhance identification of significant gene sets and pathways.
• Visualization and Exploration: Provides functions to visualize and explore identified gene sets and biological pathways.

Scientific Applications:

• Ca2+ remodeling in colorectal cancer (CRC): Applied to compare expression of 77 selected intracellular Ca2+ transport-related transcripts between normal human colonic NCM460 cells and colon cancer HT29 cells to reveal remodeling of intracellular Ca2+ homeostasis affecting voltage-operated Ca2+ channels, store-operated Ca2+ entry components, transient receptor potential (TRP) channels, Ca2+ release channels, Ca2+ pumps, Na+/Ca2+ exchanger isoforms, and mitochondrial Ca2+ transport.

Methodology:

Uses enrichment analysis integrating set-based and network-based methods on gene expression data generated by Next Generation Sequencing (NGS); in the example application mRNA from NCM460 and HT29 cells was sequenced using Ion Torrent technology, followed by data transformation, filtering, and comparative analysis of 77 selected gene transcripts.