Bidirectionally transcribed loci were defined from a set of 1,714,047 forward and 1,597,186 reverse strand CAGE tag clusters (TCs) supported by at least two CAGE tags in at least one sample (TCs defined in 6). Only TCs not overlapping antisense TCs were used. We identified 1,261,036 divergent (reverse-forward) TC pairs separated by at most 400 bp and merged all such pairs containing the same TC, while at the same time avoiding overlapping forward and reverse strand transcribed regions (prioritization by expression ranking), which resulted in 200,171 bidirectional loci (procedure illustrated in Supplementary Figure 6a). A center position was defined for each bidirectional locus as the mid position between the rightmost reverse strand TC and leftmost forward strand TC included in the merged bidirectional pair. Each bidirectional locus was further associated with two 200 bp regions immediately flanking the center position, one (left) for reverse strand transcription and one (right) for forward strand transcription, in a divergent manner. The merged bidirectional pairs were further required to be bidirectionally transcribed (CAGE tags supporting both windows flanking the center) in at least one
