The most frequent overlap length was 4 nt, followed by 1-nt overlaps.
The most frequent overlap length was 4-nt-long (short phase 2 overlap; representing approximately 45% of all overlaps), and the second most frequent overlap length was 1-nt-long (also short phase 2 overlap; representing approximately 15% of all overlaps).
The most frequent overlap of responses was 15 of those who indicated it was not necessary to tell a partner because they had protected sex, also checked off that they tell some partners that they were HIV-positive but not others.
The most frequent overlapping fingerprints were PTEN loss and KRAS mutations (co-occurring in 13 patients), and BRAF and PIK3CA mutations (in 7 patients) (Figure 1).
Chromatin accessibility, as measured by DHS, increased towards DMR midpoints and the most frequent UC DMR-DHS overlaps were observed in the H1ESC cell line.
This analysis is summarized in Additional file 3. Briefly, we calculated the probability that the frequency with which the two most frequent (and overlapping) 6mers, TCGGCA and GGCAGT, and to the most frequent 7mer, GGCAGTT (a one base extension to the second 6mer), occur at least once or twice in the upstream regions of effector genes is by chance association.
The resulting simulated and empirical overlap length distributions share four relevant features: phase 2 overlaps are more frequent than those in phase 1; the most frequent type of overlaps is short phase 2; the frequency of long overlaps decreases with the length of the overlap; and in long overlaps, those in phase 1 are more frequent.
The second to sixth most frequent pentanucleotide words overlap with UGUAA [see Additional file 2], highlighting the importance of this motif.
30 In summary, we could demonstrate that patients with overlap syndromes differ from lcSSc and dcSSc regarding lung fibrosis and heart involvement, and that musculoskeletal involvement is clearly the most frequent organ manifestation in overlap patients.
However, it is noteworthy that the most frequent form of pathological overlap between Lewy body diseases and AD is the presence of increased numbers of Aβ plaques in PDD and DLB [ 25, 33], with limited formation of tangles and the interactions between α-syn and Aβ were, therefore, the primary focus of this study.
Nevertheless, our results also indicate that major patterns in the overlapping length distribution (short phase 2 as the most frequent; long phase 1 overlaps more frequent than long phase 2) and a decay rate can be partially explained by the probability of finding frameshifted start and stop codons across a protein-coding gene and by taking into account start/stop codon redundancy.
