The SUM Cell Lines Gateway is the heart and soul of the Knowledge Base. This is the space where we present the Functional Genomics data that we generated for each of the SUM lines in a way that illuminates the biology of each cell line. Each Cell Line page contains information on how we developed the line and everything we know about the patient from which the cells came, and we also summarize what we know about the oncogenes that are likely driving their biology. Also presented in these pages are selected KEGG pathways with the hit genes from the shRNA screen mapped onto the pathways for each cell line. These files provide a picture of the relative importance of these pathways for each line. However, these files are just picture files and are meant to be an introduction to how shRNA screen data mapped to KEGG pathways provide insight into the biology of each line. Users are encouraged to move from these pages to the KEGG Pathway Engine pages where one can view both gene essentiality data and gene expression data for any cell line and for ANY KEGG pathway. In addition, the KEGG Pathway Engine shows the actual data from the screen, as well as the genomic and druggability features of any gene in the pathway that was a screen hit. I feel that this approach to presenting screen data is superior to providing long lists of hit genes by allowing easy visualization of the screen hit data in pathways of interest to breast cancer researchers. When multiple hit genes map to a pathway, this is clear evidence for an important aspect of the biology of the cells, and points to specific genes within the pathways that may be targetable. By viewing the same pathways in different cell lines, one can get a sense of the differing biology of the different cell lines, and all of this is directly related to the ultimate goal of this Knowledge Base, which is to develop novel strategies to reverse engineer breast cancer cells.
Here are the links that will take you to the Knowledge Base for each of the SUM breast cancer cell lines.
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