arrayMap

arrayMap provides a curated reference database of probe-level and processed genomic array copy-number profiles for human cancers to support analysis of somatic copy number aberrations and large-scale oncogenomic meta-analyses.

Key Features:

• Extensive Data Collection: Hosts over 64,000 genomic array datasets representing approximately 250 different tumor diagnoses derived from public repositories and curated resources.
• Probe-level Source Data and Progenetix Integration: Functions as an integral component of the Progenetix project with direct access to probe-specific genomic array read-outs during curation.
• Data Integration and Processing: Employs custom processing pipelines to integrate diverse genomic array datasets and map them to multiple human reference assemblies, including UCSC hg18 and GRCh37.
• Enhanced Data Mining Support: Provides data and resources suitable for large-scale meta-analysis and detection of complex genomic events such as chromothripsis-like patterns.
• Support for Non-public/User-provided Datasets: Supports processing of non-public and user-provided array datasets for inclusion in analyses.
• Data Visualization Capabilities: Offers visualization of array-level copy-number data to facilitate exploration of CNA patterns.

Scientific Applications:

• Meta-analysis and Systems-level Integration: Serves as an entry point for meta-analyses and systems-level integration of high-resolution oncogenomic CNA data.
• Research on Somatic CNAs: Enables comparative studies of somatic copy number aberrations across a broad spectrum of human malignancies to investigate tumorigenesis and progression.
• Exploration of Genomic Events: Facilitates investigation of complex genomic events, including chromothripsis-like patterns and related rearrangements.

Methodology:

Data are curated and processed using custom processing pipelines that integrate probe-level genomic array read-outs across diverse datasets and map them to multiple human reference genome assemblies (UCSC hg18 and GRCh37).