Fig. 3

Denoised gene expression with SEDR. A Immunofluorescence (IF) values, raw RNA-seq counts, and denoised gene expression by SEDR for PTPRC (CD45) on the ovarian cancer dataset. B Scatter plot of scaled IF values with raw counts and de-noised PTPRC expression by SEDR. C H&E image with identified germinal centers (GCs) in the lymph node tissue sample. D Denoised expression of three marker genes within the selected GCs. BCL6, FCER2, and EGR1 are the markers for different regions of GCs. E Denoised expression of IGHD and three genes that are correlated with IGHD: MS4A1 and CD1C are positively correlated with IGHD while CD3D is negatively correlated with IGHD. F Pearson correlation between IGHD and the correlated genes (MS4A1, CD1C, CD3D) as measured by raw counts, de-noised value by Sprod, and de-noised value by SEDR