Dear DepMap Community Forum,
good afternoon and I hope my message finds you well and healthy !!
Briefly, based on an international collaborative research project (Athens Comprehensive Cancer Center (ACCC)) regarding colorectal cancer, our major goal is to investigate, if there any specific functional programs in specific clinical groups of patients, that might interrelate the presence of specific mutational patterns (KRASonly, BRAFonly and wild type), as the ultimate goal is to investigate the molecular landscape of these 3 defined groups-we also utilize additionally public TCGA data to enhance our sample size-
Ultimately, based on my major post-doc project, I would like to use the DepMap portal data, in order:
A) Compare if possible KRAS-mutated cell lines versus other colorectal cancer cell lines without the KRAS mutation; the same approach also to be extended to BRAF-mutated cell lines, even to expand to specific allele-mutated samples based on the availability
B) In detail, my main goal is to identify which perturbagens/drugs might sensitize differentially these groups of cell lines, that could be associated with distinct clinical subgroups; in addition, which genes are mainly affected and/or altered in each group-this might give us an additional external validation, as from our gene expression data, we have identified separate gene signatures for each group (KRAS mut, BRAF mut etc.) and thus prioritize further specific targets;
On this premise, from the data portal, one approach would be to use the Custom analyses section, and utilize the 2-group comparison; however, is it possible for the data portal to find information for mutational status concerning colorectal cancer cell lines? In order to perform an appropriate selection and robust creation of the compared cell lines? Or I would have to use another portal?
Furthermore, as the second aim to identify the genetic dependencies-i.e. the genes-that are mostly correlated with the above drug sensitivity profiles, the most direct and robust approach would be to select from the step1 the top perturbagens, and perform a correlation analysis?
Thank you in advance for your time and consideration on this matter!!
With Kind Regards,