The knowledge base (SLKB) includes data from 11 experiments across 22 cell lines, comprising 16,059 synthetic lethality gene pairs.
Poor integration and annotation of current synthetic lethality data limit its utility.
Diverse methods for calculating synthetic lethality scores result in only 1.21% overlap among the top 10% of gene pairs.
The SL network shows a higher likelihood of connectivity among SL gene pairs compared to non-SL pairs.
Comparison of SL networks between two cell lines indicates a greater likelihood of sharing synthetic lethality hub genes rather than pairs.
Simplified
Emerging CRISPR-Cas9 technology permits (SL) screening of large number of gene pairs from (CDKO) experiments. However, the poor integration and annotation of CDKO SL data in current SL databases limit their utility, and diverse methods of calculating SL scores prohibit their comparison. To overcome these shortcomings, we have developed SL knowledge base (SLKB) that incorporates data of 11 CDKO experiments in 22 cell lines, 16,059 SL gene pairs and 264,424 non-SL gene pairs. Additionally, within SLKB, we have implemented five SL calculation methods: median score with and without background control normalization (Median-B/NB), sgRNA-derived score (sgRNA-B/NB), Horlbeck score, GEMINI score and MAGeCK score. The five scores have demonstrated a mere 1.21% overlap among their top 10% SL gene pairs, reflecting high diversity. Users can browse SL networks and assess the impact of scoring methods using Venn diagrams. The SL network generated from all data in SLKB shows a greater likelihood of SL gene pair connectivity with other SL gene pairs than non-SL pairs. Comparison of SL networks between two cell lines demonstrated greater likelihood to share SL hub genes than SL gene pairs. SLKB website and pipeline can be freely accessed at https://slkb.osubmi.org and https://slkb.docs.osubmi.org/, respectively.
Key numbers
16,059
Number of gene pairs
Total gene pairs identified from 11 experiments
1.21%
Overlap of top gene pairs
Overlap among top 10% gene pairs across five scoring methods
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