ISACGH

ISACGH integrates array comparative genomic hybridization (array-CGH) data with gene expression values to analyze copy number variations and their effects on gene expression.

Key Features:

• Integration of Genomic Data and Gene Expression: Integrates array-CGH data with gene expression datasets to correlate copy number variations with changes in gene expression.
• Functional Profiling Options: Performs functional profiling using Gene Ontology terms, pathways, and PubMed abstracts to annotate genomic regions.
• Advanced Visualization Capabilities: Generates visualizations that map genomic alterations and gene expression patterns onto chromosomal coordinates.
• Accurate Estimation Methods: Implements methods to estimate genomic copy number from array-CGH hybridization data.
• Integration with GEPAS: Integrates with the Gene Expression Profile Analysis Suite (GEPAS) for preprocessing, normalization, and downstream analysis of microarray experiments.
• DAS Server Connectivity: Provides DAS server connectivity to export results to the Ensembl viewer for contextual genomic annotation.

Scientific Applications:

• Cancer Genomics: Correlates copy number alterations with gene expression to identify candidate drivers and biomarkers in cancer.
• Genetic Disorders: Analyzes copy number variations and associated expression changes relevant to genetic disorders.
• Genomic Instability Studies: Characterizes molecular mechanisms underlying diseases with genomic instability by integrating CNV and expression data.
• Biomarker and Therapeutic Target Identification: Supports identification of potential biomarkers and therapeutic targets through integrated CNV-expression analysis.

Methodology:

Processes array-CGH data with methods to estimate copy number variations, performs normalization of microarray experiments, and conducts functional annotation using biological databases, with integration to GEPAS for preprocessing and downstream analysis.