Figure 2
Distributions of genomic features among different sequence zones.
(a) Circos diagrams for chromosomes 5 and 18 showing from outside inward positions on chromosome in Mb and abundances (Supplementary Table S4) of GENE (blue), L1 (red), Alu viz. sum of AluY, AluS, AluJ and FLAM (green), TFBS (orange), CID (purple) and MIR (yellow) in 500-kb windows expressed in separate linear scales. (b) Distributions of a number of features in 50-kb windows in the 59.50–62.50 Mb segment of chromosome 5 and their partition into 500-kb Genic, Proximal and Distal windows. (c) Bar chart plotting fractional distributions of non-Marker features among Genic, Proximal and Distal zones (as given in Supplementary Table S5) against their zonal classification based on Supplementary Table S1. Twenty-nine of the 31 features yield a correct match: 23/24 Genic features (blue underlined) show largest fractional distribution in Genic zones (blue section of bar), 4/4 Proximal features (green underlined) show largest fractional distribution in Proximal zones (green section) and 2/3 Distal (red underlined) features show largest fractional distribution in Distal zones (red section). The names of these features with correct matching are marked by bold font. The classifications of LINC and NAS-, which do not yield a correct match, are also shown by Fig. 1a and Supplementary Table S2 to be borderline: LINC forms red squares with all Group I, all Group III and some but not all Group II features; and NAS- forms blue squares with three-out-of-four features in Group I, both L1 and ATrich in Group III, but red squares with all except one (viz. SRNA+) features in Group II. Notably, the high fractional distribution of 0.887 in Genic zones displayed by SRNA- indicates that the ‘Genic’ windows identified by the feature-ratios method are highly distinct from the identified ‘Proximal’ and ‘Distal’ windows. Likewise, the low fractional distribution of 0.065 in Proximal zones displayed by SRNA+ indicates that the ‘Proximal’ windows identified are highly distinct from the identified ‘Genic’ and ‘Distal’ windows.
