CellMiner: a relational database and query tool for the NCI-60 cancer cell lines

Abstract

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/).

Figure 1

Schematic representation of CellMiner. CellMiner was constructed using four data resources (associated data). The user submits a job to CellMiner via a user-friendly web interface, and the job is then processed in background. Upon completion, results are returned to the user in a new HTML page or can be exported to various formats. CellMiner is publicly available at .

Figure 2

Illustrative screen shot of the CellMiner graphical user interface. Shown is the result of a "Cell Line Metadata" query on a user-selected CNS tissue subset. Included in the output are literature citations for information on the lines selected. The default selection is the entire NCI-60. The results shown here resulted from background processing of the job and display via the graphical web interface.

Figure 3

Screen shot of the "Query Datasets" input page. Shown is the result of a "Query Datasets" on a user-selected query options available to extract molecular profile data from CellMiner.

Figure 4

Screen shot of the "Query Datasets" result page. An illustrative output page displaying results of a complex "Query Datasets" search. For this particular output, the query was constructed for TP53 (identified by HUGO name) to include two datasets containing Gene symbols and chromosome numbers.