THE SUM CANCER CELL LINE KNOWLEDGE BASE
The SLKBase is your comprehensive resource for the SUM series of human breast cancer cell lines, originally developed in the Ethier laboratory at the University of Michigan. Our database has expanded to include a panel of 50 other commonly used breast cancer lines, and over 900 additional human cancer cell lines across all types. In total, the Knowledge Base provides integrated functional genomics and drug sensitivity data for over 1,000 human cancer models.
With regard to the SUM series of human breast cancer cell lines, here is what you’ll find in these pages:
- A brief description of how each of the SUM cell lines was derived, including information on the patient from whom the cells were isolated.
- A summary of some of the key features of the SUM cell line panel
- The protocols for care and feeding of the SUM breast cancer cell lines.
- A description of the key genomic features that drive the biology of each cell line.
- A description of the genome-scale shRNA screen that we performed for all of the SUM lines, as well as in MCF-7, MCF-7LTED cells, and MCF-10A cells. This functional screen allows for the identification of the essential genes for the proliferation and survival of each of the cell lines.
- A narrative summary for each SUM cell line in which I describe some of the key findings that are relevant to each cell line based on the shRNA screen data, the functional oncogene signature, and the gene expression data sets for each cell line.
- A discussion of the functional oncogene signature for each cell line.
- A description of the functional druggable signatures for each of the SUM lines
- A bibliography listing published papers that contain data obtained with each of the SUM cell lines.
A series of powerful data mining tools/apps that can be used to explore the SUM cell lines, as well as over 1000 other human cancer cell lines. The specific apps are:
- A Gene Query app that allows all investigators to determine the status of any gene in any of the over 1000 cancer cell lines. Data retrieved by this app includes copy number, expression level, mutation status, and essentiality data for any gene in any cell line.
- An Oncogene Signature and Drug Sensitivity app that allows investigators to quickly identify the key oncogenes that are genomically altered in any cell line, and then, by clicking a button, view the drug sensitivity data for over 700 targeted cancer drugs in any cell line.
- A KEGG Pathway Engine allows users to choose any KEGG pathway for any cell line and map the gene expression data onto the pathway. In addition, one can map the gene essentiality data, determined by either CRISPR or RNAi screens, onto the pathway of interest. In this way, users can analyze the significance of any specific KEGG pathway in the biology of each cell line.
To explore the Knowledge Base for each cell line, use the banner above or click here to get to the SUM Cell Line Gateway Page, the Gateway page for the other breast cancer cell lines, or the page for analysis of all cancer cell lines.
Click here to go to the YouTube video and data download center for the SUM cell lines.
Tutorials are presented that describe how the shRNA screens were performed and how to use the KEGG pathway engine. There is also a blog that describes the pros and cons of these two types of essentiality screens.
Other features of the Knowledge Base
- A description of our views on why it’s important to have a breast cancer cell line knowledge base?
- A description of the Omic data sets that we used to develop the Knowledge Base?
- A description of our Functional Genomics Strategy for cancer cell lines
- A PowerPoint presentation that describes the functional genomics strategy and the on the development of the genomic data sets, as well as the functional genomic data sets that we used to generate the pathways.
- See what we’ve been working on to make the Knowledge Base even better.
- Click here to join the SLKBase email list on MailChimp.
- About Steve Ethier.
Frequently Asked Questions
What is SLKBase?
SLKBase (the SUM Cancer Cell Line Knowledge Base) is a curated resource originally developed to support research with the SUM series of human breast cancer cell lines. It has expanded to include an additional 50 breast cancer cell lines and over 900 cancer models across all cancer types, integrating genomics, essentiality, and drug sensitivity datasets.
Which cell lines are covered?
The Knowledge Base contains detailed pages for the SUM series, plus a broader breast cancer panel and more than 900 other human cancer cell lines. Each SUM line page includes derivation notes, key genomic features, culture protocols, shRNA screen results, and bibliographies.
What interactive tools are available?
Key apps include the Gene Query, Oncogene Signature & Drug Sensitivity viewer, and the KEGG Pathway Engine. Note: advanced SQL queries and R‑Shiny web apps require registration.
Where should I start?
Start at the SUM Cell Line Gateway for SUM-specific pages, the breast cancer panel gateway for other breast cancer cell lines, or the all-cancer gateway for the broader collection. Tutorials and a YouTube video/data download center help users navigate the data-mining tools.
How should I cite SLKBase resources?
Cite the original publications and resources associated with the SUM lines or the specific datasets you download. Each SUM cell line page includes a bibliography listing published papers that used those lines.
If you have additional questions not covered here, please contact us or consult the SLKBase documentation and tutorials.
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