ArticleCell reports methods2022
Extracting functional insights from loss-of-function screens using deep link prediction.
Article in Cell reports methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed.
- HROB is a novel prognostic biomarker correlated with immune cell infiltration and tumor progression in lung adenocarcinoma.World journal of surgical oncology · 2025Article
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5 authors.
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Abstract
We present deep link prediction (DLP), a method for the interpretation of loss-of-function screens. Our approach uses representation-based link prediction to reprioritize phenotypic readouts by integrating screening experiments with gene-gene interaction networks. We validate on 2 different loss-of-function technologies, RNAi and CRISPR, using datasets obtained from DepMap. Extensive benchmarking shows that DLP-DeepWalk outperforms other methods in recovering cell-specific dependencies, achieving an average precision well above 90% across 7 different cancer types and on both RNAi and CRISPR data. We show that the genes ranked highest by DLP-DeepWalk are appreciably more enriched in drug targets compared to the ranking based on original screening scores. Interestingly, this enrichment is more pronounced on RNAi data compared to CRISPR data, consistent with the greater inherent noise of RNAi screens. Finally, we demonstrate how DLP-DeepWalk can infer the molecular mechanism through which putative targets trigger cell line mortality.
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