Table 2

Correlation between sequence and expression profile similarities

Tissue

expression

matrixb


Sequence similarity matrixa

all KRAB-ZNF

8q24.3 KRAB-ZNF

Non-8q24.3 KRAB-ZNF


cDNA

0.27

0.62

0.15

Protein

0.39

0.62

0.38

ZNF

0.42

0.56

0.42

KRAB

0.22

0.71

0.16


a Sequence similarity matrices are based on ClustalW alignments (IUB matrix for DNA or Gonnet matrix for protein sequences) and distance calculations using the Tamura-Nei method on DNA or the Poisson correction on the amino acid level, respectively, with the pairwise deletion option; calculated with MEGA4 (see Methods). Based on whole cDNA or full protein sequence or the ZNF or KRAB protein domains only.

b Tissue expression matrices were calculated from the relative quantitative RT-PCR data using Pearson correlation distance.

Values represent Pearson correlation coefficients of matrix similarity comparisons (see Methods). All correlations are statistically significant (T-test, p < 0.0005), except cDNA and KRAB versus non-8q24.3 KRAB-ZNF (p = 0.068 and 0.062). Note that only ZNF genes with expressed KRAB domain from Figure 3 and available gene expression data were included.

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

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