Figure 6.

Evaluation of the conservation of the C2H2 ZNF DNA binding domains. (A) Principal component analysis of ZNF domains for conservation based on the 8-amino acid region from -2 to 6 with respect to the start of the α-helix of each finger (see text). Included are all individual fingers from the 8q24.3 ZNF proteins and their mouse and rat orthologs. The plot shows the first (PC1) against the second (PC2) principal component representing the variation in position 5 and 6 or -2 and 1, respectively. Negative values are indicative of lower variability and thus higher conservation. Plot areas that contain the same or similar 8-residue regions are boxed. Conserved amino acids are highlighted in single letter code at respective positions. Dashes indicate non-conserved residues. Additional file 7 details all peptides and their values/coordinates based on the boxed areas. (B) Pairwise ZNF matrix similarities between the 8q24.3 ZNF locus members (see text). Numbers in red indicate lowest values, i.e. highest similarities of each ZNF gene. (C) Detail of a paralog network founded on pairwise ZNF sequence similarities between all human C2H2 ZNF genes (see text). Nodes represent the individual genes (labeled by name), the edges describe their similarity. The thickness of the edges is proportional to the similarity and the value is given as label. A decrease in the value means an increase in similarity. Shown are the isolated 8q24.3 and 19q13.2 clusters of the network with 8q24.3 ZNF member nodes in red, and nodes of 19q13.2 members included in Figure 2 in blue. Network restricted to similarity values ≤ 2.01.

Lorenz et al. BMC Genomics 2010 11:206   doi:10.1186/1471-2164-11-206
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