TABLE 1.
Curated databases and library-based screening data.
| Data sources | Data description |
|---|---|
| Curated databases | |
| DepMap depmap portal (2021) | Dependency Map: loss-of-function (LoF) screens by Project Achilles of the Broad Institute, cell-line multi-omics by the Cancer Cell Line Encyclopedia (CCLE), and drug-sensitivity profiles by PriSM. https://depmap.org/portal/ |
| DRIVE McDonald et al. (2017) | Large-scale short hairpin RNA (shRNA) screens on 7837 genes across 398 cell lines with CCLE features. https://oncologynibr.shinyapps.io/drive/ |
| SGD Skrzypek and Nash (2015) | Saccharomyces genome database: yeast genome sequences, functional annotations, expression profiles, gene–gene interactions; includes over 10,000 synthetic lethal interactions for more than 6600 genes. https://www.yeastgenome.org/ |
| SynLethDB 2.0 Wang et al. (2022b) | Synthetic lethal pairs and non-synthetic lethal pairs for human, fly, worm, mouse, and yeast, including the gene identification numbers of the National Center for Biotechnology Information (NCBI), PubMed ID of the study, the source that classified the gene-pair interaction, and the statistical score between 0 (low) to 1 (high). Recently updated from version 1.0, the databases now house a total of 50,868 interactions for 13,707 genes. http://synlethdb.sist.shanghaitech.edu.cn/v 2/ |
| SLKG Zhang et al. (2021) | Synthetic lethality knowledge graph: 19,987 synthetic lethal pairs and 3039 synthetic dosage lethal (SDL) pairs with SL score between 0 (low) and 1 (high) calculated from 11 external databases (DRIVE, DepMap and SynLethDB,…). https://www.slkg.net/ |
| Library-based genomic screenings and multi-omics profiling data | |
| TCGA Tomczak et al. (2015) | The Cancer Genome Atlas pan-cancer database: 85,415 patient samples (33 major cancer types) with microarrays, DNA sequencing, tissue imaging, methylation (Micheel et al., 2018) (137). https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga |
| CCLE Barretina et al. (2012); Broad Institute (2005) | Cancer cell line encyclopedia: gene expression (1389 cell lines), mutation (1755 cell lines), and copy number (1750 cell lines). https://sites.broadinstitute.org/ccle/ |
| GTEx Lonsdale (2013) | Genotype-tissue expression project: gene expression for different tissue types (17,382 samples over 948 donors in 54 non-diseased tissues) using both bulk-cell and single-cell gene profiles. https://gtexportal.org/home/ |
| Specialized datasets | Curated microarray database (CuMiDa) (Feltes et al., 2019): 78 human microarray datasets curated from the Gene Expression Omnibus (GEO) https://sbcb.inf.ufrgs.br/cumidaBARRA:CuRDa (Feltes et al., 2021): 17 human RNA-seq datasets curated from the GEO https://sbcb.inf.ufrgs.br/barracurdaCancerSCEM (Zeng et al., 2022): 208 single-cell RNA-sequencing samples from 28 studies, covering 20 human cancer types https://ngdc.cncb.ac.cn/cancerscem/ |
| Data Sources: synthetic lethality screening based on single-gene perturbation | ||||
| Data sources | Library size | Target | Technology | Cell line/s |
| Astsaturov et al. (2010) | Targeting 638 genes with two siRNAs for each gene | EGFR | siRNA screen with chemical inhibitors | A431 |
| Bommi-Reddy et al. (2008) | 100 shRNAs targeting 88 kinases | Von Hippel-Lindau (VHL) | shRNA screen | 786-O (WT), RCC4 (VHL−/−) |
| Lord et al. (2008) | Human DNA repair siRNA set V1.0 (siRNA library containing 230 DNA repair genes). | PARP and DNA repair genes | siRNA screen with PARPi | CAL51 |
| Turner et al. (2008) | siRNA library targeting 779 human protein kinase and kinase-related genes. | Human protein kinase and kinase-related genes | siRNA screen with PARPi | CAL51 |
| Luo et al. (2009) | 74,905 retroviral shRNAs targeting 32,293 unique human transcripts. | KRAS | GW shRNA screen | DLD-1 Ras WT, DLD-1 Ras Mut |
| Martin et al. (2009) | 1200 drugs and drug-like molecules | MSH2 | Gene mutation with chemical inhibitor screening | Hec59 (MSH2 deficient), Hec59 + chr2 (MSH2 proficient, WT) |
| Marcotte et al. (2012a) | 78,432 shRNAs targeting 16,056 Ref-seq genes (O'Leary et al., 2016). | Ref-seq genes | shRNA screen | 29 breast, 28 pancreatic, 15 ovarian cancer cell lines |
| Steckel et al. (2012) | 7000 siRNA pools targeting the druggable human genome (∼7400 genes). | KRAS | shRNA screen | HCT116 (KRAS mut), HKE-3 (WT) |
| Toyoshima et al. (2012) | siRNAs targeting 3300 druggable genes and 200 microRNAs. | MYC | siRNA screen | HFF-MYC (overexpression), HFF-PBabe (control) |
| Vizeacoumar et al. (2013) | 78,432 unique shRNAs targeting 16,056 human genes. | PTTG1, BLM, MUS81, PTEN, KRAS | siRNA screen | HCT116 with derived phenotypes of PTTG1−/−, BLM−/−, MUS81−/−, PTEN−/−, KRAS+/− |
| Boettcher et al. (2014) | Pooled shRNAs targeting 10,000 genes, together with siRNAs targeting fumarate hydratase (FH). | Fumarate hydratase | shRNA and siRNA screen | HEK293T, UOK262 |
| Shen et al. (2015) | Targeting 112 known tumor-suppressor genes. | CHEK1/2 | siRNA screen with chemical inhibitor AZD7762 | HeLA (treated with siRNAs together with AZD7762 versus DMSO) |
| Pathak et al. (2015) | 1276 siRNAs targeting 638 genes | A network centered on EGFR, HER2, BCAR1, NEDD9, and EFS | siRNA screen with chemical inhibitor dasatinib | A1847 |
| Synthetic lethality screening based on combinatorial perturbations | |||
| Combinatorial perturbation studies | Library size | Synthetic lethality biology | Cell lines (disease versus normal) |
| Laufer et al. (2013) | 51,680 siRNA combinations that come from 323 epigenetic regulator genes | Epigenetic regulation genes | HCT116 |
| Wang et al. (2014) | 6032 siRNA pairs of 1508 gene pairs | Genes with frequent alterations in breast cancer | MCF10A |
| Wong et al. (2016) | 50 genes, 23,409 gRNA pairs | Epigenetics regulation | OVCAR8 |
| Han et al. (2017) | 207 genes, 21,321 gRNA pairs | Non-essential drug targets | K562 |
| Shen et al. (2017) | 73 genes, 141,912 gRNA pairs | Drug targets | HeLa, 293T, A549 |
| Horlbeck et al. (2018) | 472 genes, 111,392 gene pairs | Non-essential genes | K562, Jurkat |
| Zhao et al. (2018) | 51 genes,11,475 gRNA pairs | Metabolic network | HeLa, A549 |
| Ito et al. (2021) | 3284 genes, 5065 paralog pairs | Paralog families | 11 cancer cell lines |
| Parrish et al. (2021) | 2060 gene pairs | Paralog families | PC9, HeLa |
| Diehl et al. (2021) | 160 genes, 12,736 gene pairs | Autophagy pathway | HEK293T, RPE1 |
| Thompson et al. (2021) | 1191 gene pairs | Paralog families | A375, MeWo, RPE1 |