Supplementary Table S7 from A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution

Supplementary Table S7: SIDP results (MCF7 & LTED) summary. S7.1: regions showing at least one overlapping sgRNA scoring in at least one of the different conditions assayed. For each region (hg38 genomic coordinates), the table indicates whether this was selected as a gene promoter, putative enhancer, or putative insulator. It also shows the symbol of the nearest gene, and the distance to its TSS in bp (positive or negative values indicate the region is either downstream or upstream the TSS, respectively). For each condition (MCF7 +E2, MCF7 -E2 or LTED) and direction of the change (DF vs IF), the table indicates whether the region overlaps one or more (columns labeled “single”) vs two or more (columns labeled “multiple”) sgRNAs. S7.2: summary of the overlaps between either scoring sgRNAs (“guides”), regions showing at least one scoring sgRNA (“regions_single”), or regions showing two or more consistently scoring sgRNAs (“regions_multiple”) between pairs of conditions (as indicated by columns assay_1 and assay_2). The nature of the change (either DF or IF), along with the total number of overlapping sgRNAs or regions, and the corresponding fraction, are also indicated. S7.3: results of gene set enrichment analysis using the indicated gene sets and the set of genes close to the regions showing scoring sgRNAs, according to the indicated pattern (SIDP_set). Statistics of the hyper-geometric test are shown, along with the total number of the overlapping genes (count), the observed and expected overlaps, and the odds ratio. S7.4: total number of regions showing multiple, consistent, scoring sgRNAs, and relative split-up based on the distance (bp) to the nearest TSS (0-0.5 kbp, 0.5-2.5 kbp, 2.5-5 kbp, 5-10 kbp, over 10 kbp), per condition (MCF7 +E2, MCF7 -E2 or LTED) and direction of the change (DF vs IF).