Supplementary Table S16 from A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution

Supplementary Table S16: Downstream analyses considering only the SIDV inferred genetic alterations with predicted impact on function. S16.1: results of the binomial enrichment test. SID regions overlapping at least 2 SNVs predicted as pathogenic are included. Along with genomic coordinates (hg38) the total number of SNVs as well as the number of predicted pathogenic SNVs overlapping the region are indicated. The p-value and the q-value (after Benjamini-Hochberg correction) of the binomial test are indicated, along with annotation to the closest gene. The 63 regions considered for further analyses are highlighted in red. S16.2: same as S13.1 but considering all the regions assigned to the genes annotated to the same ontological terms together. The number and identity of the genes contributing to the overlap are indicated, along with p-value of the binomial test, and the q-value (after Benjamini-Hochberg correction). Statistically significant terms (q-value <= 0.05) are highlighted in red. S16.3: results of the analyses testing for the enrichment of mutations (either SNVs, short INDELs, or both; mutation_type column) with computationally predicted pathogenic effects in the sets of regions also showing a certain behavior in SIDP (CRISPRi_hit_type column). Observed and expected overlap are indicated, along with the odds ratio and the p-value (Chi-squared test).