THE SUM BREAST 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), and to a panel of 50 other commonly used breast cancer cell lines
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 series of Data Mining Tools that can be used to explore the SUM lines as well as the 50 other breast cancer cell lines. These tools allow users to probe deeply into each cell line and determine the key genes and pathways for each line, and to identify the essential genes that are druggable. These tools allow users to rank order KEGG pathways for any cell line based on their essentialness, as determined by the shRNA screen, and their druggablity. There is an Oncogene Signature tool, a Gene Query tool and a Proteomics tool that allows users to probe any gene and retrieve all of the genomic and functional genomic data for that gene in all the cell lines. All of the tools can be accessed by clicking here.
- A gene query tool allows users to investigate the status of any gene of interest in any of the cell lines.
- A KEGG Pathway Engine allows users to analyze the significance of specific KEGG pathways and the hit genes in the pathways in the biology of each cell line. Users can access the KEGG pathways associated screen data in two ways:
- By clicking on the KEGG pathway page associated with each cell line
- By using the KEGG pathway engine, which allows users to analyze any KEGG pathway, and search for any gene of interest for all of the cell lines.
- A bibliography listing published papers that contain data obtained with each of the SUM cell lines.
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
Tutorials are presented that describe how the shRNA screens were performed, and how to use the KEGG pathway engine.
Thus, the SUM Line Knowledge Base (SLKBase) will allow users of any of the SUM cell lines to obtain a deeper understanding of the cell lines they are working with, which will allow each user to put their own research findings into context with everything that is known about each cell line.
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 Power Point presentation on the development of the genomic data sets, as well as the functional genomic data sets that we used to generate the pathways.
- A series of blog posts on areas of interest related to the development of the SUM breast cancer cell lines.
- Blog space for each of the cell lines and we hope that users of the lines will post comments related to their findings and experience with the cell lines. One goal of the Knowledge Base is to develop a community of users who interact with each other to accelerate the pace of research in breast cancer.
