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simplifyenrichment:A Bioconductor Package for Clustering and Visualizing Functional enrichment Results

Genomics, Proteomics & Bioinformatics 2023年第1期21卷 190-202页

作者： Zuguang Gu Daniel Hübschmann Molecular Precision Oncology Program National Center for Tumor Diseases(NCT)HeidelbergD-69120 HeidelbergGermany Heidelberg Institute of Stem Cell Technology and Experimental Medicine(HI-STEM) D-69120 HeidelbergGermany German Cancer Consortium(DKTK) D-69120 HeidelbergGermany Department of Pediatric Immunology Hematology and OncologyUniversity Hospital HeidelbergD-69120 HeidelbergGermany

Functional enrichment analysis or gene set enrichment analysis is a basic bioinformatics method that evaluates the biological importance of a list of genes of interest.However,it may produce a long list of significant terms with highly redundant information that is difficult to summarize.Current tools to Simplify enrichment results by clustering them into groups either still produce redundancy between clusters or do not retain consistent term similarities within clusters.We propose a new method named binary cut for clustering similarity matrices of functional terms.Through comprehensive benchmarks on both simulated and real-world datasets,we demonstrated that binary cut could efficiently cluster functional terms into groups where terms showed consistent similarities within groups and were mutually exclusive between groups.We compared binary cut clustering on the similarity matrices obtained from different similarity measures and found that semantic similarity worked well with binary cut,while similarity matrices based on gene overlap showed less consistent patterns.We implemented the binary cut algorithm in the R package simplifyenrichment,which additionally provides functionalities for visualizing,summarizing,and comparing the clustering.The simplifyenrichment package and the documentation are available at https://***/packages/simplifyenrichment/.

关键词： Functional enrichment Simplify enrichment Clustering R/Bioconductor Software Visualization

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