Extended Data Fig. 1: HDAC6 score in BC.

(a) The number of samples and dataset of origin used to evaluate the HDAC6 regulon. (b) Overlap of the original and updated HDAC6 regulons. P value was estimated using two-tailed Fisher’s exact test. N was determined by the total number of genes for network inference. (c) The network plot of HDAC6 and updated HDAC6 regulon. Edge width is corresponding to the correlation strength measured by mutual information. Red and blue edges indicate positive and negative correlations between HDAC6 and each of the regulon genes. The table below shows the pathway enrichment of the genes in the regulon, showing its association with unfolded protein response. P value was estimated using two-tailed Fisher’s exact test. (d) New HDAC6 score comparing IBCs vs non-IBCs. (e) HDAC6 scores of all BCs from TCGA and METABRIC are divided into molecular subtypes. (f) HDAC6 scores in 45 ductal metastatic breast cancer samples from the MBC Project divided into histological molecular subtypes. In d, e and f, the center line indicates the median value. The lower and upper hinges represent the 25th and 75th percentiles, respectively, and whiskers denote 1.5x interquartile range; the red line represents the median of the HDAC6 scores in IBC samples and the numbers over each whisker plot indicate the percentage of samples over this value in each clinical subtype. Sample size (n = number of samples) of each group was indicated in the axis labels. P value was estimated using two-tailed t test.