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Fig. 1 | Genome Biology

Fig. 1

From: xCell: digitally portraying the tissue cellular heterogeneity landscape

Fig. 1

xCell study design. a A summary of the data sources used in the study to generate the gene signatures, showing the number of pure cell types and number of samples curated from them. b Our compendium of 64 human cell type gene signatures grouped into five cell type families. c The xCell pipeline. Using the data sources and based on different thresholds, we derived gene signatures for 64 cell types. Of this collection of 6573 signatures, we chose the 489 most reliable cell types, three for each cell type from each data source where available. The raw score is then the average single-sample GSEA (ssGSEA) score of all signatures corresponding to the cell type. Using simulations of gene expression for each cell type, we derived a function to transform the non-linear association between the scores to a linear scale. Using the simulations we also derive the dependencies between cell type scores and apply a spillover compensation method to adjust the scores

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