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The SLKBase is always a work in progress, and we are constantly striving to improve the site and make it more useful to users of the SUM lines. Here’s what we done recently to increase the power of the SLKBase, and a taste of what’s on the horizon:
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We have added more functional screening data to our MySQL database so that the KEGG pathway engine and Gene Query tool can be used for all of the SUM lines, and also for MCF-7 cells, MCF-7LTED cells, and MCF-10A cells. The MCF-7LTED (long term estrogen-deprived) cell line that was developed in the Daniel Birnbaum lab at INSERM, Marseille, France. These same data mining tools can also be used to explore the 50 other breast cancer cell lines in our database.
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We have obtained proteomic and phospho-proteomic data for all of the SUM lines using reverse phase protein arrays from the MD Anderson proteomics core laboratory. Using that data, we have now added a proteomics page to each of the SUM cell line home pages that shows protein and phospho-protein expression data for selected proteins in each line. We also added a proteomics search tool which can be find under the Data Mining Tools for the SLKBase tab. Using this tool, one can obtain the proteomic and phosphoproteomic data for everything that is on the RPPA array and see the data for any cell line.
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We have improved the Gene Query tool that allows users to retrieve data for any gene from all of the cell lines in the data base, instead of one cell line at a time. The generated list shows the data for the searched gene in each cell line and the cell lines are rank-ordered by their essentialness as determined in the shRNA screen. Thus, one can see at a glance the relative essentialness of the searched gene in all of the cell lines. This tool also shows the genomic features of each gene, it’s expression level in each cell line, and any targeted drug that exists for that gene.
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We have added full functional genomic data to our database for over 900 cancer cell lines of all types and functional genomic and drug sensitivity analysis can now be performed on any of these cell lines.
Want more? Let us know!
