Resolution:
## Figure 1.
Quantification of expression conservation by local network similarity (LNS). Pair-wise Pearson correlation between genes was calculated for individual S. bayanus and S. cerevisiae datasets, generating a matrix of gene-gene correlations. The data used to create
this illustration are the actual diauxic shift, cell cycle synchronization, and alpha
factor treatment. The distribution of these correlation values is between −1 and 1,
and can be drastically different from one dataset to another. Therefore, Fisher’s
z-transformation and normalization of these z-values were applied on each correlation
matrix, so that the correlations were comparable across datasets. The resulting correlation
matrices are normally distributed and centered at 0 with standard deviation equal
to 1. For each orthologous pair i and i’, their z-transformed, normalized correlation to all other matched orthologs form
two vectors, indicating the relative positions of this pair of ortholog in their respective
expression network. The correlation of these two vectors was taken as LNS. To calculate
the correlation matrix for global LNS, the average values of individual datasets for
a specific gene-gene pair were used to form a new global correlation matrix. According
to the properties of normal distribution, the values within this matrix are still
normally distributed and centered at 0 with standard deviation equal to 1. This global
matrix was then used to calculate global LNS for each ortholog. To simulate the case
of non-conservation, orthologous pairs were randomized along one axis of the expression
correlation matrix. Therefore in calculating background LNS, only the ortholog match
was disturbed, but not the expression network structure (in contrast to randomizing
along both axes).
Guan |