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This portal contains genomic data and drug response data for the cell lines in the
Human Glioma Cell Culture (HGCC) collection (Johansson, Krona, Kundu et al, Cell Reports, 2020).
The data are made available in three complementary formats:
as data files (e.g. expression matrices) for download and analysis.
interactively, in the below gene and drug browser. Instructions
To use the gene and drug browser, enter a gene symbol of interest or look up a drug of interest in the list.
After the data has been fetched from our server, you can choose between a table view, a boxplot view, a scatter plot view, a survival view, and a dose-response view.
Note that most drugs are best predicted by a combination of biomarkers, so the association between individual variables and drug response should not be over-interpreted.
To visualize the network in Cytoscape, download the Cytoscape file and open it in a recent version of Cytoscape.
The primary network is dense, as it contains all connections between drugs, different genomic biomarkers, and hallmark pathways.
We recommend filtering the network in Cytoscape using the select function.
Please note that the subtype calling methodology sometimes differ between the Xie et al., and Johansson et al. publications because a more general algorithm (based on the consensus over multiple methods) was used in the latter. In addition to the choice of computational methodology, subtype of a cell line can be influenced by biological and experimental factors. Also, the mutation calls are based on consensus calling over 4 different programs. Mutations called by at least 3/4 programs are shown in the paper. The web visualisation is more conclusive, showing 2/4 callers. This will be visualised in future versions of the web interface.
