GeneSetR: Genome Wide Perturb-Seq based Gene Set Analyzer
Omer Faruk Kuzu (Researcher, Saatcioglu Group, BMB, IBV)
Identification of genotype-phenotype relationships is of utmost importance and a core effort in biology. Recent developments in efficient and precise gene targeting approaches coupled to significant technological advances in next generation sequencing and mass spectrometry, including in single cells, such as in Perturb-Seq, have made dramatic improvements in deciphering phenotypic consequences of gene targeting approaches. However, analysis of the resulting large data sets remains a significant challenge. Many single gene perturbations can affect the activity of hundreds of other genes. In addition, current methods for identifying key genes or pathways, such as gene set enrichment analysis (GSEA) and clustering methods, have significant limitations. For example, GSEA suffers from bias and poor curation of gene lists, while clustering approaches solely rely on expression patterns that are influenced by many different factors. Here we present Perturb-Seq based Gene Set Analyzer (GeneSetR), a user-friendly web-server that can analyze user-defined gene lists based on the data from a recently published genome-wide Perturb-seq study. Through this tool, users can cluster gene lists of their choice following dimensionality reduction by various approaches, generate heat maps based on perturbation or gene expression data, undertake pathway analysis from RNA sequencing data, identify key nodes among the submitted genes, and perform gene signature analyses. GeneSetR enables researchers to readily identify gene clusters associated with specific phenotypes or biological processes, providing insights into the functional roles of these clusters and the role of single genes in them. With its user-friendly interface and robust analysis capabilities, GeneSetR is a free resource for the analysis of genome-wide Perturb-Seq data and the exploration of novel genotype-phenotype relationships.