The most pervasive method for identifying the sources of variation in scRNA-seq studies is principal component analysis (PCA) 6, 7, 8. The vectors derived from GeneVector provide a framework for identifying metagenes within a gene co-expression graph and relating these metagenes back to each cell using latent space arithmetic. While current methods reduce dimensionality with respect to sparse expression across each cell, our tool produces a lower dimensional embedding with respect to each gene. Inspired by such work, we developed a tool that generates gene vectors based on single cell RNA (scRNA)-seq expression data. Similar methodology has been applied to bulk RNA-seq expression for finding co-expression patterns 5. To find contextually similar words, NLP methods make use of vector space models to represent similarities in a lower dimensional space. NLP commonly uses dimensionality reduction to identify word associations within a body of text 3, 4. To find similarities in lower dimensions, biology can borrow from the field of natural language processing (NLP). However, to map existing biological knowledge to each cell, the derived features must be interpretable at the gene level. The first intuitive step to identify such co-regulated genes is the reduction of dimensionality for sparse expression measurements: high dimensional gene expression data is compressed into a minimal set of explanatory features that highlight similarities in cellular function. To approximate these connections, transcriptomic studies have conceptually organized the transcriptome into sets of co-regulated genes, termed gene programs 1 or metagenes 2. Maintenance of cell state and execution of cellular function are based on coordinated activity within networks of related genes. In this work, we show in four single cell RNA-seq datasets that GeneVector was able to capture phenotype-specific pathways, perform batch effect correction, interactively annotate cell types, and identify pathway variation with treatment over time. Unlike other methods, including principal component analysis and variational autoencoders, GeneVector uses latent space arithmetic in a lower dimensional gene embedding to identify transcriptional programs and classify cell types. We describe GeneVector, a scalable framework for dimensionality reduction implemented as a vector space model using mutual information between gene expression. By performing dimensionality reduction with respect to gene co-expression, low-dimensional features can model these gene-specific relationships and leverage shared signal to overcome sparsity. However, current dimensionality reduction methods aggregate sparse gene information across cells, without directly measuring the relationships that exist between genes. Private individuals seeking a more economical or passenger-friendly alternative might want to consider the Dodge Sprinter.Deciphering individual cell phenotypes from cell-specific transcriptional processes requires high dimensional single cell RNA sequencing. Naturally, these attributes are most often needed by small businesses and fleet operators. The 2007 Chevrolet Express still outpaces the aged Econoline and certainly warrants consideration for those who need the immense passenger capacity (up to 15 people can ride in an Express 3500) and cargo volume only a large van can provide. A number of important under-the-skin changes took place for 2003, including a wider selection of V8 engines, the first-time availability of all-wheel drive, upgraded brakes, a stronger frame and various interior improvements - all of which went a long way toward making the Express safer and more capable than ever before. To celebrate the rebirth, the van's name was changed from "Sportvan" to "Express." A new exterior look, new engines, extended body styles and improved ergonomics soon made the Chevrolet Express hard to overlook when compared with Ford's dated Econoline. Still, it rode on the same basic platform that it had had since the swinging '60s until a complete frame-up redesign took place in 1996. Having been around for more than four decades, Chevrolet's full-size van lived through the '70s, '80s and half of the '90s via sheet metal changes and updates to the running gear.
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