Co-essentiality browser — what this tool is

This site hosts an interactive browser of gene co-essentiality in cancer research. It is built on the data of the study «A genome-wide almanac of co-essential modules assigns function to uncharacterized genes» (bioRxiv 827071, 2019) by Akshay Balsubramani and colleagues. Co-essentiality means that two genes tend to be needed for cell survival in the same cancer cell lines; genes with similar essentiality profiles usually work in the same biological module or pathway.

The landscape map below places 17,634 human genes so that genes with matching essentiality patterns across 485 cancer cell lines of the CCLE/DepMap 18Q3 release sit close together. Each point is one gene, labelled by its HGNC symbol; colours mark annotated clusters. The essentiality scores come from genome-wide CRISPR/shRNA dropout screens; mutation and RNA expression data from the same CCLE/DepMap release annotate the selected genes, and protein-protein interaction context comes from STRING v11.0.

How to use it

1. Drag on the landscape with Box Select or Lasso to mark a group of genes (at most 200 per selection).
2. Choose Plot essentiality to draw the heatmap of essentiality scores for the selected genes across the cell lines, grouped by tissue of origin.
3. Pick a gene in the dropdown to read its full HGNC name and annotations; the selected-gene box lists the current graph selection.
4. Run the enrichment panel to test the selection against current gProfiler annotations at a 0.05 significance threshold across ten source families (GO, KEGG, Reactome and others).

Historical scientific browser running the original local gene data: file upload, saved-set controls and layout download are unavailable in this original-source release.