Progenetix: 12 years of oncogenomic data curation

TL;DR

Progenetix has expanded its oncogenomic database over 12 years, offering extensive CNA profiles, new analysis tools, and improved user interfaces to aid cancer research.

Contribution

This paper details the 12-year development of Progenetix, including data growth, new visualization tools, and enhanced user interfaces for cancer genome analysis.

Findings

Over 60-fold increase in cancer samples in Progenetix.

Introduction of gene-specific CNA frequency analysis tools.

Enhanced user interface for data processing and visualization.

Abstract

DNA copy number aberrations (CNAs) can be found in the majority of cancer genomes, and are crucial for understanding the potential mechanisms underlying tumor initiation and progression. Since the first release in 2001, the Progenetix project (http://www.progenetix.org) has provided a reference resource dedicated to provide the most comprehensive collection of genome-wide CNA profiles. Reflecting the application of comparative genomic hybridization (CGH) techniques to tens of thousands of cancer genomes, over the past 12 years our data curation efforts have resulted in a more than 60-fold increase in the number of cancer samples presented through Progenetix. In addition, new data exploration tools and visualization options have been added. In particular, the gene specific CNA frequency analysis should facilitate the assignment of cancer genes to related cancer types. Additionally, the new user file processing interface allows users to take advantage of the online tools, including various data representation options for proprietary data pre-publication. In this update article, we report recent improvements of the database in terms of content, user interface and online tools.