| 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. |