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Updated: Oct 28, 2025
07:41
Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases
Published on: May 17, 2019
9.2K
The Progenetix oncogenomic resource in 2021.
Qingyao Huang1,2, Paula Carrio-Cordo1,2, Bo Gao1,2
1Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland.
Summary
Progenetix curates extensive cancer copy number aberration (CNA) profiles, significantly increasing data accessibility. This resource empowers integrative analyses of tumor genome variations for cancer research.
Area of Science:
- Genomics
- Cancer Research
- Bioinformatics
Background:
- Copy number aberrations (CNAs) are common in cancer, driving tumorigenesis and influencing molecular subtypes.
- Cancer genomic profiling projects have generated vast amounts of data, but it is often fragmented across studies.
- Integrative analysis of large genomic variant collections is crucial for understanding cancer biology.
Purpose of the Study:
- To present the Progenetix resource, a comprehensive collection of cancer CNA profiles and metadata.
- To highlight advancements in data integration, quality, and accessibility for cancer genomics research.
- To facilitate comparative and meta-analyses of cancer genome variations.
Main Methods:
- Curating individual cancer CNA profiles and associated metadata from published studies and repositories.
- Continuous data integration, curation, and maintenance of the Progenetix database.
- Updating database schemas and enhancing data access through a new web front-end and programmatic access.
Main Results:
- The Progenetix resource now contains 138,663 CNA profiles (115,357 tumor profiles), a 4.5-fold increase since 2013.
- Significant improvements in data quality and ontology representation, including a CNV landscape summary across 51 NCI Thesaurus cancer terms.
- Enhanced data access via a new web front-end and programmatic access.
Conclusions:
- Progenetix provides the most comprehensive representation of cancer genome CNA profiling data available.
- The resource empowers integrative analyses across diverse cancer biologies.
- Advancements facilitate deeper insights into cancer molecular mechanisms and subtypes through enhanced data accessibility.
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