SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality

TL;DR

SL-Miner is a web tool that helps identify and prioritize cancer-specific synthetic lethal gene pairs using evidence and visualizations.

Contribution

SL-Miner introduces a user-friendly platform for mining and prioritizing cancer-specific synthetic lethality with integrated evidence.

Findings

SL-Miner integrates various evidence types to prioritize candidate synthetic lethal gene pairs.

The tool provides intuitive visualizations like volcano and box plots for data interpretation.

It addresses the lack of evidence and user-friendliness in existing synthetic lethality prediction methods.

Abstract

Synthetic lethality (SL) refers to a type of genetic interaction in which the simultaneous inactivation of two genes leads to cell death, while the inactivation of a single gene does not affect cell viability. It significantly expands the range of potential therapeutic targets for anti-cancer treatments. SL interactions are primarily identified through experimental screening and computational prediction. Although various computational methods have been proposed, they tend to ignore providing evidence to support their predictions of SL. Besides, they are rarely user-friendly for biologists who likely have limited programming skills. Moreover, the genetic context specificity of SL interactions is often not taken into consideration. Here, we introduce a web server called SL-Miner, which is designed to mine the evidence of SL relationships between a primary gene and a few candidate SL partner genes in a specific type of cancer, and to prioritize these candidate genes by integrating various types of evidence. For intuitive data visualization, SL-Miner provides a range of charts (e.g. volcano plot and box plot) to help users get insights from the data.

SL-Miner is available at https://slminer.sist.shanghaitech.edu.cn.

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