As expected, duplications of universal domains positively correlated with duplications of universal protein families (r = 0.96, p = 4.50E-10), as did their deletions (r = 0.93, p = 8.35E-8 8.35E-8
The expected duplication frequency of segmental and tandem duplication events in each family was calculated as follows: For tandem counts, a simulation was carried out, placing N genes of size 1 kb (where N is the size of the corresponding gene family) in a genome of approximately 100000 kb and counting how many pairs of genes were within a 50 kb window.
We defined genes with increased copy number as those with a log2 aCGH ratio greater than 0.7 (because relative intensity values are often slightly compressed from the expected duplication log2 value of 1.0); genes with a log2 aCGH ratio < −1.0 were identified as potentially deleted.
As expected, the duplication of bi-lobe and the bi-lobe-associated Golgi was inhibited.
In the SERK and SERKL genes there is not a simple ratio of two soybean genes for every Medicago gene, as would be expected from simple duplication of the soybean genome.
From these frequencies, we will obtain the expected number of duplication events among different autosomes, from the Z to the autosomes and from the autosomes to the Z, which we can then compare with the observed gene movements.
No families fall below one standard deviation below the median in both the segmental and tandem categories, but several are close: the mitochondrial carrier proteins and the heat shock transcription factor families have 9%and13%3% of the expected segmental duplications, respectively.
Each pathway was tested for deviation from expected levels of gene duplication via χ2 analysis with the P values tested for significance under an FDR of 0.05 (Table S4).
However, the global effect following CDK11 RNAi was a centriole duplication defect and not an over duplication as expected in case of Plk4 overexpression.
Based on the observation of increased size of gene families in vertebrates [ 10, 33- 40] and their highly specialized tissues, we expected to find duplications of entire pathways in the vertebrate lineage.
