ArticleGenomics, proteomics & bioinformatics2024
MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data.
Article in Genomics, proteomics & bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- EMMA-STRAT: a multi-omics based machine learning framework for stratification of endometrial carcinoma molecular subtypes and MSI status.BioData mining · 2026Article
- Intratumoral heterogeneity in microsatellite instability status at single-cell resolution.iScience · 2026Article
- Analysis of microsatellite instability intensity in single-cell resolution with scMnT reveals tumor heterogeneity in colorectal cancer.Briefings in bioinformatics · 2026Article
- Single-cell multi-omics characterize colorectal tumors, adjacent healthy tissue and matched (tumor) organoids identifying CRC-unique features.International journal of cancer · 2025Article
- Performance assessment of computational tools to detect microsatellite instability.Briefings in bioinformatics · 2024Article
- Detecting microsatellite instability by length comparison of microsatellites in the 3' untranslated region with RNA-seq.Briefings in bioinformatics · 2024Article
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Authors and funding
6 authors.
Funding
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Abstract
Microsatellite instability (MSI) is an indispensable biomarker in cancer immunotherapy. Currently, MSI scoring methods by high-throughput omics methods have gained popularity and demonstrated better performance than the gold standard method for MSI detection. However, the MSI detection method on expression data, especially single-cell expression data, is still lacking, limiting the scope of clinical application and prohibiting the investigation of MSI at a single-cell level. Herein, we developed MSIsensor-RNA, an accurate, robust, adaptable, and standalone software to detect MSI status based on expression values of MSI-associated genes. We demonstrated the favorable performance and promise of MSIsensor-RNA in both bulk and single-cell gene expression data in multiplatform technologies including RNA sequencing (RNA-seq), microarray, and single-cell RNA-seq. MSIsensor-RNA is a versatile, efficient, and robust method for MSI status detection from both bulk and single-cell gene expression data in clinical studies and applications. MSIsensor-RNA is available at https://github.com/xjtu-omics/msisensor-rna.
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