bc-GenExMiner

bc-GenExMiner analyzes breast cancer transcriptomic data to perform differential gene expression analyses and comparative studies across cohorts and triple-negative breast cancer subtypes.

Key Features:

• Data integration: Incorporates 62 breast cancer cohorts and one healthy breast cohort with clinicopathological annotations and combines microarray and RNA-seq transcriptomic data.
• Expression module: Implements a statistical mining "Expression" module to facilitate extensive differential gene expression analyses.
• Differential gene expression analyses: Supports 39 differential expression analyses organized into 13 categories based on clinicopathological and molecular characteristics, enabling targeted, exhaustive, or customized studies.
• Comparative analysis: Compares gene expression across healthy (cancer-free), tumour-adjacent, and tumour tissues and within three triple-negative breast cancer subtypes: C1 (molecular apocrine tumours), C2 (basal-like tumours infiltrated by immune suppressive cells), and C3 (basal-like tumours triggering an ineffective immune response).
• Visualization: Presents analysis results in four distinct plot types.
• Validation: Employs validation tests that confirm bioinformatics processes do not alter the pathobiological information of source data.

Scientific Applications:

• Exploratory transcriptomic analysis: Enables exploration of differential gene expression patterns across breast cancer cohorts and tissue types.
• Cross-cohort validation: Allows validation of gene expression findings across multiple cohorts with clinicopathological annotations.
• Subtype-specific investigation: Supports comparative studies focused on triple-negative breast cancer subtypes C1, C2, and C3.
• Translational research support: Provides data and analyses applicable to both basic research and clinical research applications.

Methodology:

Uses microarray and RNA-seq transcriptomic data analyzed by the statistical mining "Expression" module to perform differential gene expression analyses; validation tests assess preservation of pathobiological information.