Extended Data Fig. 2: Interspecies Point Projection combines bridged alignments and synteny to identify orthologous regions. | Nature Genetics

Extended Data Fig. 2: Interspecies Point Projection combines bridged alignments and synteny to identify orthologous regions.

From: Conservation of regulatory elements with highly diverged sequences across large evolutionary distances

Extended Data Fig. 2

(a) Classification of direct and bridged alignments through the use of intermediate species (b) Increase in the number of anchor points and distance to the nearest anchor points through multi-species bridged alignments. Comparison between 0, 1 and 15 bridging species (c) Classifcation of projections as directly and indirectly conserved. DC regions overlap a sequence alignment or are ▯ 300 bp from a direct alignment. The distance of IC regions as >300 bp but ▯ 2.5 kb from a direct or indirect alignment. Regions with >2.5 kb summed distance through the species graph from anchor points are classified as NC. (d) Fractions of mouse enhancers identified as directly conserved (DC, blue) or either directly or indirectly conserved (DC + IC, orange) as a function of the projection score threshold. Fraction of functionally conserved DC + IC elements as a function of the projection score threshold (red). Solid lines = enhancers, dashed lines = randomly selected background regions. Dotted vertical lines represent DC threshold score of 0.979 and IC of 0.841.

Back to article page