![]() In the case of transcriptomics, prior knowledge is typically rendered as gene sets containing genes belonging to, e.g., the same biological process or to the same Gene Ontology (GO) annotation. įunctional analysis tools typically combine prior knowledge with a statistical method to gain functional and mechanistic insights from omics data. These functional analysis tools are broadly used and belong to the standard toolkit to analyze expression data. To extract functional and mechanistic information from these profiles, many tools have been developed that can, for example, estimate the status of molecular processes such as the activity of pathways or transcription factors (TFs). Thanks to diverse high-throughput techniques, such as microarrays and RNA-seq, expression profiles can be collected relatively easily and are hence very common. Gene expression profiles provide a blueprint of the status of cells. Furthermore, we find that the performance of functional analysis tools is more sensitive to the gene sets than to the statistic used. Our analyses suggest that bulk-based functional analysis tools that use manually curated footprint gene sets can be applied to scRNA-seq data, partially outperforming dedicated single-cell tools. We also provide the benchmark data for further use by the community. Additionally, we show that the TF and pathway activities preserve cell type-specific variability by analyzing a mixture sample sequenced with 13 scRNA-seq protocols. Our benchmarks on simulated and real data reveal comparable performance to the original bulk data. ![]() We complement the simulated data with real scRNA-seq data upon CRISPR-mediated knock-out. For the in silico study, we simulate single cells from TF/pathway perturbation bulk RNA-seq experiments. We include the bulk-RNA tools PROGENy, GO enrichment, and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compare them against the tools SCENIC/AUCell and metaVIPER, designed for scRNA-seq. To address this question, we perform benchmark studies on simulated and real scRNA-seq data. ![]() It is thus not clear if functional TF and pathway analysis tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way. However, scRNA-seq data has characteristics such as drop-out events and low library sizes. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. The School offers a range of undergraduate and postgraduate qualifications validated by the University of the West of England and the acting and stage management courses are accredited by the National Council for Drama Training.Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. The School is an affiliate of the Conservatoire for Dance and Drama. The School also tours productions around the West Country and to Bristol schools. Performance venues in Bristol are established public theatres including the Bristol Old Vic, Redgrave Theatre, The Alma Pub Theatre and other venues. The School is housed in large premises overlooking Clifton Downs and in the former BBC Christchurch Studios, which offers unparalleled facilities for radio and television work. The School has close working partnerships with national and local producing companies, consistently achieving 100% graduate employment. The School is staffed by experienced working professionals and trains people for all disciplines, working together within one “producing house’ organisation. Work encompasses the breadth of theatre, television, radio, film, recording, events and trade presentations and the ever-increasing areas of employment open to a trained work-force in the Arts and Entertainment Industry. ![]() Opened by Laurence Olivier in 1946, the School is an Industry-led vocational training establishment preparing students for careers in acting, stage management, costume, design, scenic art, directing, theatre arts management, production management, lighting, electrics, sound, studio management, propmaking, VT editing and scenic construction. ![]() We attract the very best talent in students and staff, and our courses are recognised nationally and internationally as a benchmark of quality in professional acting, technical, production and management training. ![]()
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