Datasets Used

Resource Description Key Insights Terms / abbreviations
DGE RNA-seq We collected high throughput RNA-seq following knockout or inhibition of individual DUBs. 81 DUB knockouts and 7 inhibitors were characterized. The transcriptomic signatures following loss of individual DUBs.

"3’DGE-seq: 3’ Digital Gene Expression, a type of high-throughput RNA-seq.

DE gene: differentially expressed gene (defined by a false discovery rate (FDR) adjusted p < 0.05)."

Connectivity Map (CMap) A Broad Institute database of post-perturbation RNA-seq signatures following genetic knockdown or over-expression or treatment with inhibitors. The signatures within this resource are comprised of the L1000 genes (1000 genes measured or inferred by the assay). Data are available for ~3,000 different genes and ~5000 small molecules. Enables identification of genes that, when silenced with RNAi, or overexpressed, have similar transcriptional effects as query signatures (e.g., signatures following DUB knockout).

"Query mRNA profile: the transcriptomic signature that the user inputs into CMap to retrieve similar signatures.

A tau score quantifies similarity between the query mRNA profile and CMap signatures (tau similarity is computed by counting the number of pairwise mismatches between two ranked lists). CMap recommends a threshold of tau similarity score > 90."

Dependency Map (DepMap) Broad Institute genome-wide pooled CRISPR-Cas9 knockout screen conducted in more than 700 cancer cell lines. Guide RNA dropout is measured as a surrogate for viability.

"Enables identification of genes that are essential for cell proliferation as well as which gene knockouts yield similar viability phenotypes across cell lines (co-dependent genes).

The top co-dependent genes can be analyzed to identify protein complexes and pathways enriched in the co-dependent genes."

"Genes with similar DepMap scores across cell lines are more likely to have related biological functions, a property known as co-dependency.

Co-dependent genes: gene knockouts that exhibit co-dependency or give similar DepMap scores across cell lines. In our study, we analyzed the top seven co-dependent genes as this gave the largest number of expected results for well-characterized DUBs, but the top five and ten co-dependent genes gave similar results. "

Cancer Cell Line Encyclopedia (CCLE) Proteomics Previously published baseline proteomics collected in the CCLE cell lines (~375 cell lines). About 12,000 proteins were detected. Co-expressed genes based on expression levels across ~375 cell lines. Proteins in the same complex are often co-expressed to a significant degree across a cell line panel. Co-expressed genes: correlation in abundance across cell lines with FDR < 0.01 and |z-score| > 2. Previous publication used FDR < 0.01.
BioGRID Protein-protein interaction database compiling interaction data from multiple sources. Proteins that interact as measured in multiple ways, including affinity capture MS, affinity capture Western Blotting, and assembly of reconstituted complexes from purified recombinant subunits in vitro. PPID: protein-protein interaction database.
IntAct Protein-protein interaction database compiling interaction data from multiple sources. Proteins that interact as measured in multiple ways, including affinity capture MS, affinity capture Western Blotting, and assembly of reconstituted complexes from purified recombinant subunits in vitro. PPID: protein-protein interaction database.
NURSA Protein-protein interaction dataset focused on interactions among proteins involved in transcription. Proteins that interact as measured by ~3000 immuno-precipitations (IPs) followed by MS. "PPID: protein-protein interaction database.