Fig. 1

BETA is robust to the number of differentially-expressed genes, but sensitive to gene expression changes: (a) Comparison of transcriptional profiles from DCs stimulated with Interferon-β for 2.5 h and unstimulated DCs identified 884 differentially-expressed genes. Varying numbers of genes (x-axis) were randomly sampled from this set. For each of these cases, ISGF3 activity was measured by BETA (left y-axis and empty triangles) and hypergeometric test P values (right y-axis and empty circles) (b) Starting from the transcriptional profile of un-stimulated DCs, ISGF3 activity was simulated by computationally increasing the expression levels of ISGs, defined by Schoggins et. al. [31], from 8 to 85 % above their baseline values (x-axis). ISGF3 activity was then measured by BETA (y-axis, with grey area indicating 95 % confidence intervals) using a gene set based on the V$ISRE_01 matrix from TRANSFAC. P-values ISGF3 activity are 3.00e-1, 2.12e-13 and 1.07e-13