Fig. 1

Systems Architecture diagram of the components of the GSEPD system, with major sections in red outlines. Blue items indicate automated systems. An experiment starts at the upper left, with the Sequencing Facility where the tissue samples are converted to gene expression quantification through sequencing and processing external to GSEPD. The user then creates a table of count data and defines the sample metadata and conditions to be compared (lower left, green items indicate user inputs). Across the top are External Resources, where functional annotation databases are curated by third parties and plug in to the rgsepd software package. The R code wraps subprocesses for differential expression, set enrichment, and set based projection scoring. The orange cylinder of sample data indicates a normalization produced by DESeq2 with useful expression measurements. Within the Projection Engine box are small diagrams of the integral vector projections and clustering analyses