G  E  A  R

Genome-wide Enrichment Analysis for Regional DNA Copy Number Changes

INTRODUCTION

  The genomic alterations commonly observed in human solid tumors have been thought to contribute to the genesis and progression of the disease primarily by altering the activities of cancer-related genes. In spite of the recent advancement in the detection of copy number changes such as array-based comparative genomic hybridization (array-CGH) or similar high-resolution platforms (oligonucleotide-based array-CGH), extensive and complex nature of chromosomal alterations in tumor genome has made it difficult to select and functionally interpret biologically relevant changes in systematic perspectives. GEAR (Genome-wide Enrichment Analysis for Regional DNA copy number changes) have been developed to functionally analyze the genome-wide alterations detected by array-CGH results by adopting 'functional enrichment (or pathway) analysis'. Using GEAR, the prevalent genomic imbalances observed in human solid tumors are interpreted as the coordinated genomic dosage changes of functionally related genes, collectively termed as genomic signatures. It is based on the assumption that genome-wide chromosomal alterations might affect the activities of hundreds to thousands of genes the majority of which, if not all, may produce wide spectrum of molecular events while such coordinated changes cannot be detectable by conventional single gene approaches. Since the annotated functions of genomic signatures are suggestive of the processes associated with the genesis or development of tumors, GEAR can lead to the identification of key functions that are activated or repressed in the corresponding tumor genomes for better insights on the tumorigenesis and also for the advanced strategies in diagnosis and therapy.

            - GEAR software installing package - Download

            - After download, execute SETUP.msi to install GEAR package
              (test datasets of array-CGH, gene mapping and pathway files are included)

            - For simple running of enrichment analysis, PERL package is provided DOWNLOAD

            - GEAR technical report and instructions (require Acrobat Reader) - Download

            - Statistical considerations and related issues (with FAQ) for GEAR algorithm - ReadMe

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