SLKBase!

THE SUM CANCER CELL LINE KNOWLEDGE BASE

This is your one stop resource for knowledge, data, and information relevant to the SUM series of human breast cancer cell lines, developed in the Ethier laboratory at the University of Michigan (SUM= Steve’s University of Michigan cells), to a panel of 50 other commonly used breast cancer cell lines, and to a group of over 900 human cancer cell lines of all cancer types.  Thus, the Knowledge Base can be used to access the functional genomics and drug sensitivity data for over 1000 human cancer cell lines.

With regard to the SUM series of human breast cancer cell line, Here is what you’ll find in these pages:

  • A brief description of how each of the SUM cell lines were derived, including information on the patient from which the cells were isolated.
  • A summary of some of the key features of 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 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 the over 1000 other human cancer cell lines.  The specific apps are:

  • A Gene Query app that all allows 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, mutations 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 and for any cell line, 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.  Users can access the KEGG pathways associated screen data in two ways:

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.

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

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