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CellMiner: a relational database and query tool for the NCI-60 cancer cell lines
Uma T Shankavaram1, Sudhir Varma, David Kane
1Genomics & Bioinformatics Group, Laboratory of Molecular Pharmacology, Centre for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA. Uma.Shankavaram@nih.hhs.gov
Background:
Advances in the high-throughput omic technologies have made it possible to profile cells in a large number of ways at the DNA, RNA, protein, chromosomal, functional, and pharmacological levels. A persistent problem is that some classes of molecular data are labeled with gene identifiers, others with transcript or protein identifiers, and still others with chromosomal locations. What has lagged behind is the ability to integrate the resulting data to uncover complex relationships and patterns. Those issues are reflected in full form by molecular profile data on the panel of 60 diverse human cancer cell lines (the NCI-60) used since 1990 by the U.S. National Cancer Institute to screen compounds for anticancer activity. To our knowledge, CellMiner is the first online database resource for integration of the diverse molecular types of NCI-60 and related meta data.
Description:
CellMiner enables scientists to perform advanced querying of molecular information on NCI-60 (and additional types) through a single web interface. CellMiner is a freely available tool that organizes and stores raw and normalized data that represent multiple types of molecular characterizations at the DNA, RNA, protein, and pharmacological levels. Annotations for each project, along with associated metadata on the samples and datasets, are stored in a MySQL database and linked to the molecular profile data. Data can be queried and downloaded along with comprehensive information on experimental and analytic methods for each data set. A Data Intersection tool allows selection of a list of genes (proteins) in common between two or more data sets and outputs the data for those genes (proteins) in the respective sets. In addition to its role as an integrative resource for the NCI-60, the CellMiner package also serves as a shell for incorporation of molecular profile data on other cell or tissue sample types.
Conclusion:
CellMiner is a relational database tool for storing, querying, integrating, and downloading molecular profile data on the NCI-60 and other cancer cell types. More broadly, it provides a template to use in providing such functionality for other molecular profile data generated by academic institutions, public projects, or the private sector. CellMiner is available online at (http://discover.nci.nih.gov/cellminer/).
Insights
CellMiner integrates diverse molecular data from the NCI-60 cancer cell lines, enabling complex pattern discovery. This novel database facilitates research by linking gene, transcript, and protein identifiers for advanced analysis.
Area of Science:
- Bioinformatics
- Genomics
- Cancer Research
Background:
- High-throughput omic technologies generate diverse molecular data (DNA, RNA, protein, etc.).
- Integrating these data types, particularly for the NCI-60 cancer cell lines, presents a significant challenge.
- Existing methods struggle to link gene, transcript, protein, and chromosomal identifiers.
Purpose of the Study:
- To introduce CellMiner, the first online database for integrating diverse molecular data types of the NCI-60.
- To provide a unified platform for querying and analyzing multi-omic data from cancer cell lines.
- To offer a template for integrating molecular profile data from various sources.
Main Methods:
- CellMiner utilizes a MySQL database to store and link raw and normalized multi-omic data.
- A single web interface allows advanced querying of DNA, RNA, protein, and pharmacological data.
- Includes a Data Intersection tool for identifying common genes/proteins across datasets.
Main Results:
- CellMiner successfully integrates diverse molecular profiles for the NCI-60.
- Enables querying and downloading of integrated data with experimental metadata.
- Provides a framework for incorporating other cell or tissue sample types.
Conclusions:
- CellMiner is a relational database tool for NCI-60 molecular data integration, querying, and downloading.
- It serves as a template for integrating diverse molecular profiles from public and private sources.
- The tool is freely available online to facilitate cancer research.