Supplementary tables for "Analysis of RNA processing directly from spatial transcriptomics data reveals previously unknown regulation"

<em>Table 1: Dataset summary. </em>Columns are: dataname (name of dataset), num_spots (the number of Visium spots with tissue information), med_reads_per_spot (median number of reads per spot), SpliZ_med_per_spot (median number of genes with SpliZ values per spot), ReadZS_med_per_spot (median number of 5000-bp windows with ReadZS values per spot), ge_med_per_spot (median number of genes with nonnegative gene expression per spot), and ReadZS_ge_med_per_spot (median number of 5000-bp windows with nonnegative gene expression per spot) <br> <em>Table 2: Summary of discoveries. </em>Columns are: dataname (name of dataset), score (either ReadZS_norm, SpliZ_norm, ge_norm, which is gene expression, or ReadZS_ge_norm, which is 5000-bp-window expression), num_genes (the number of genes tested, or windows in the case of ReadZS_norm or ReadZS_ge_norm), num_sig (the number with significant spatial patterns by Moran’s I), top (the top 10 genes/windows found to be significant in the dataset for the given score), and frac_sig (the fraction of significant genes or windows). <br> <em>Table 3: Spatial score (Moran’s I) for each gene/window in each dataset</em>. A) Scores for the SpliZ. B) Scores for the ReadZS. C) Scores for gene expression. D) Scores for gene expression by genomic window. Columns are: gene (gene name), window (genomic window identifier; use Table 4 to decode), score_cont (Moran’s I score), num_pairs (number of neighboring pairs with non-NA values for this gene/window in this dataset), perm_pvals_emp_adj (empirical permutation p value, adjusted by Benjamini Hochberg correction), dataname (name of the dataset). <br> <em>Table 4:</em> <em>Mapping of genomic windows to gene names.</em> A) Mapping for mouse data. B) Mapping for human data. Columns are: chr (chromosome), start (beginning coordinate of the window), end (ending coordinate of the window), window (the name assigned to the genomic window), strand (the genomic strand), gene (the gene name(s) assigned to this window and strand).